生成pdb格式的文件在gview里转换为gjf格式，Gaussian计算一直报错

0.01 · 发表于 Post on 2025-2-6 13:21:21

我是生成pdb格式的文件在gview里转换为gjf格式的，下边是输入文件
%chk=C:\Users\asus\Desktop\new2.chk
#p B3LYP/6-31G* nosymm

Title Card Required

0 1
N(PDBName=N,ResName=MOL,ResNum=1_A)                5.71500000 3.98900000 1.70000000
N(PDBName=N,ResName=MOL,ResNum=1_A)                1.55000000 3.28700000 1.70000000
C(PDBName=C,ResName=MOL,ResNum=1_A)                4.32800000 3.67500000 1.70000000
C(PDBName=C,ResName=MOL,ResNum=1_A)                3.79000000 2.38100000 1.70000000
H(PDBName=H,ResName=MOL,ResNum=1_A)                4.44300000 1.51600000 1.70000000
C(PDBName=C,ResName=MOL,ResNum=1_A)                2.40500000 2.25100000 1.70000000
H(PDBName=H,ResName=MOL,ResNum=1_A)                1.95000000 1.26200000 1.70000000
C(PDBName=C,ResName=MOL,ResNum=1_A)                3.45300000 4.76400000 1.70000000
H(PDBName=H,ResName=MOL,ResNum=1_A)                3.85000000 5.77400000 1.70000000
C(PDBName=C,ResName=MOL,ResNum=1_A)                2.08000000 4.51500000 1.70000000
H(PDBName=H,ResName=MOL,ResNum=1_A)                1.37300000 5.34200000 1.70000000
N(PDBName=N,ResName=MOL,ResNum=1_A)                6.47300000 2.98500000 1.70000000
N(PDBName=N,ResName=MOL,ResNum=1_A)                10.63800000 3.68800000 1.70000000
C(PDBName=C,ResName=MOL,ResNum=1_A)                7.86000000 3.29900000 1.70000000
C(PDBName=C,ResName=MOL,ResNum=1_A)                8.39900000 4.59400000 1.70000000
H(PDBName=H,ResName=MOL,ResNum=1_A)                7.74500000 5.45800000 1.70000000
C(PDBName=C,ResName=MOL,ResNum=1_A)                9.78300000 4.72400000 1.70000000
H(PDBName=H,ResName=MOL,ResNum=1_A)                10.23800000 5.71300000 1.70000000
C(PDBName=C,ResName=MOL,ResNum=1_A)                8.73600000 2.21000000 1.70000000
H(PDBName=H,ResName=MOL,ResNum=1_A)                8.33800000 1.20000000 1.70000000
C(PDBName=C,ResName=MOL,ResNum=1_A)                10.10900000 2.45900000 1.70000000
H(PDBName=H,ResName=MOL,ResNum=1_A)                10.81600000 1.63200000 1.70000000

1 3 1.0 12 2.0
2 6 1.5 10 1.5
3 4 1.5 8 1.5
4 6 1.5 5 1.0
5
6 7 1.0
7
8 9 1.0 10 1.5
9
10 11 1.0
11
12 14 1.0
13 21 1.5 17 1.5
14 19 1.5 15 1.5
15 16 1.0 17 1.5
16
17 18 1.0
18
19 20 1.0 21 1.5
20
21 22 1.0
22

输出文件
%chk=C:\Users\asus\Desktop\new2.chk
----------------------
#p B3LYP/6-31G* nosymm
----------------------
1/38=1,172=1/1;
2/12=2,15=1,17=6,18=5,40=1/2;
3/5=1,6=6,7=1,11=2,25=1,30=1,74=-5/1,2,3;
4//1;
5/5=2,38=5/2;
6/7=2,8=2,9=2,10=2,28=1/1;
99/5=1,9=1/99;
Leave Link 1 at Thu Feb 06 12:52:25 2025, MaxMem=          0 cpu:             0.0 elap:             0.1
(Enter C:\Gaussian\G16W\l101.exe)
-------------------
Title Card Required
-------------------
Symbolic Z-matrix:
Charge =  0 Multiplicity = 1
N(PDBName=N,ResName=MOL,ResNum=1_A)  5.715    3.989    1.7
N(PDBName=N,ResName=MOL,ResNum=1_A)  1.55    3.287    1.7
C(PDBName=C,ResName=MOL,ResNum=1_A)  4.328    3.675    1.7
C(PDBName=C,ResName=MOL,ResNum=1_A)  3.79    2.381    1.7
H(PDBName=H,ResName=MOL,ResNum=1_A)  4.443    1.516    1.7
C(PDBName=C,ResName=MOL,ResNum=1_A)  2.405    2.251    1.7
H(PDBName=H,ResName=MOL,ResNum=1_A)  1.95    1.262    1.7
C(PDBName=C,ResName=MOL,ResNum=1_A)  3.453    4.764    1.7
H(PDBName=H,ResName=MOL,ResNum=1_A)  3.85    5.774    1.7
C(PDBName=C,ResName=MOL,ResNum=1_A)  2.08    4.515    1.7
H(PDBName=H,ResName=MOL,ResNum=1_A)  1.373    5.342    1.7
N(PDBName=N,ResName=MOL,ResNum=1_A)  6.473    2.985    1.7
N(PDBName=N,ResName=MOL,ResNum=1_A)  10.638 3.688    1.7
C(PDBName=C,ResName=MOL,ResNum=1_A)  7.86    3.299    1.7
C(PDBName=C,ResName=MOL,ResNum=1_A)  8.399    4.594    1.7
H(PDBName=H,ResName=MOL,ResNum=1_A)  7.745    5.458    1.7
C(PDBName=C,ResName=MOL,ResNum=1_A)  9.783    4.724    1.7
H(PDBName=H,ResName=MOL,ResNum=1_A)  10.238 5.713    1.7
C(PDBName=C,ResName=MOL,ResNum=1_A)  8.736    2.21    1.7
H(PDBName=H,ResName=MOL,ResNum=1_A)  8.338    1.2    1.7
C(PDBName=C,ResName=MOL,ResNum=1_A)  10.109 2.459    1.7
H(PDBName=H,ResName=MOL,ResNum=1_A)  10.816 1.632    1.7

ITRead=  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
ITRead=  0  0
MicOpt= -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
MicOpt= -1 -1
NAtoms=    22 NQM=    22 NQMF=    0 NMMI=    0 NMMIF=    0
            NMic=    0 NMicF=    0.
Error parsing secondary structure:
QPErr --- A syntax error was detected in the input line.
  1 3 1.0 12 2.0
  '
Last state= "Top"
TCursr=    101 LCursr=       1
Error termination via Lnk1e in C:\Gaussian\G16W\l101.exe at Thu Feb 06 12:52:25 2025.
Elapsed time:    0 days  0 hours  0 minutes  0.3 seconds.
File lengths (MBytes):  RWF=    6 Int=    0 D2E=    0 Chk=    1 Scr=    1
因为我是想框出长宽高，所以我也试了另一种方式，就是把pdb格式导入multiwfn生成Gaussian input文件，
输入文件
%chk=new.chk
#p B3LYP/6-31G* nosymm

Generated by Multiwfn

  0  1
N    5.71500000 3.98900000 1.70000000
N    1.55000000 3.28700000 1.70000000
C    4.32800000 3.67500000 1.70000000
C    3.79000000 2.38100000 1.70000000
H    4.44300000 1.51600000 1.70000000
C    2.40500000 2.25100000 1.70000000
H    1.95000000 1.26200000 1.70000000
C    3.45300000 4.76400000 1.70000000
H    3.85000000 5.77400000 1.70000000
C    2.08000000 4.51500000 1.70000000
H    1.37300000 5.34200000 1.70000000
N    6.47300000 2.98500000 1.70000000
N    10.63800000 3.68800000 1.70000000
C    7.86000000 3.29900000 1.70000000
C    8.39900000 4.59400000 1.70000000
H    7.74500000 5.45800000 1.70000000
C    9.78300000 4.72400000 1.70000000
H    10.23800000 5.71300000 1.70000000
C    8.73600000 2.21000000 1.70000000
H    8.33800000 1.20000000 1.70000000
C    10.10900000 2.45900000 1.70000000
H    10.81600000 1.63200000 1.70000000
Tv 12.188000 0.000000 0.000000
Tv 0.000000 6.974000 0.000000
Tv 0.000000 0.000000 3.400000

输出文件
%chk=new.chk
----------------------
#p B3LYP/6-31G* nosymm
----------------------
1/38=1,172=1/1;
2/12=2,15=1,17=6,18=5,40=1/2;
3/5=1,6=6,7=1,11=2,25=1,30=1,74=-5/1,2,3;
4//1;
5/5=2,38=5/2;
6/7=2,8=2,9=2,10=2,28=1/1;
99/5=1,9=1/99;
Leave Link 1 at Thu Feb 06 13:01:23 2025, MaxMem=          0 cpu:             0.0 elap:             0.1
(Enter C:\Gaussian\G16W\l101.exe)
---------------------
Generated by Multiwfn
---------------------
Symbolic Z-matrix:
Charge =  0 Multiplicity = 1
N                   5.715    3.989    1.7
N                   1.55    3.287    1.7
C                   4.328    3.675    1.7
C                   3.79    2.381    1.7
H                   4.443    1.516    1.7
C                   2.405    2.251    1.7
H                   1.95    1.262    1.7
C                   3.453    4.764    1.7
H                   3.85    5.774    1.7
C                   2.08    4.515    1.7
H                   1.373    5.342    1.7
N                   6.473    2.985    1.7
N                   10.638 3.688    1.7
C                   7.86    3.299    1.7
C                   8.399    4.594    1.7
H                   7.745    5.458    1.7
C                   9.783    4.724    1.7
H                   10.238 5.713    1.7
C                   8.736    2.21    1.7
H                   8.338    1.2    1.7
C                   10.109 2.459    1.7
H                   10.816 1.632    1.7
Tv                   12.188 0.       0.
Tv                   0.       6.974    0.
Tv                   0.       0.       3.4

ITRead=  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
ITRead=  0  0  0  0  0
MicOpt= -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
MicOpt= -1 -1 -1 -1 -1
NAtoms=    25 NQM=    25 NQMF=    0 NMMI=    0 NMMIF=    0
            NMic=    0 NMicF=    0.
                  Isotopes and Nuclear Properties:
(Nuclear quadrupole moments (NQMom) in fm**2, nuclear magnetic moments (NMagM)
  in nuclear magnetons)

  Atom       1          2          3          4          5          6          7          8          9       10
IAtWgt=       14       14       12       12          1       12          1       12          1       12
AtmWgt=  14.0030740  14.0030740  12.0000000  12.0000000 1.0078250  12.0000000 1.0078250  12.0000000 1.0078250  12.0000000
NucSpn=          2          2          0          0          1          0          1          0          1          0
AtZEff= 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
NQMom= 2.0440000 2.0440000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
NMagM= 0.4037610 0.4037610 0.0000000 0.0000000 2.7928460 0.0000000 2.7928460 0.0000000 2.7928460 0.0000000
AtZNuc= 7.0000000 7.0000000 6.0000000 6.0000000 1.0000000 6.0000000 1.0000000 6.0000000 1.0000000 6.0000000

  Atom       11       12       13       14       15       16       17       18       19       20
IAtWgt=          1       14       14       12       12          1       12          1       12          1
AtmWgt= 1.0078250  14.0030740  14.0030740  12.0000000  12.0000000 1.0078250  12.0000000 1.0078250  12.0000000 1.0078250
NucSpn=          1          2          2          0          0          1          0          1          0          1
AtZEff= 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
NQMom= 0.0000000 2.0440000 2.0440000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
NMagM= 2.7928460 0.4037610 0.4037610 0.0000000 0.0000000 2.7928460 0.0000000 2.7928460 0.0000000 2.7928460
AtZNuc= 1.0000000 7.0000000 7.0000000 6.0000000 6.0000000 1.0000000 6.0000000 1.0000000 6.0000000 1.0000000

  Atom       21       22
IAtWgt=       12          1
AtmWgt=  12.0000000 1.0078250
NucSpn=          0          1
AtZEff= 0.0000000 0.0000000
NQMom= 0.0000000 0.0000000
NMagM= 0.0000000 2.7928460
AtZNuc= 6.0000000 1.0000000
Leave Link  101 at Thu Feb 06 13:01:24 2025, MaxMem= 104857600 cpu:             0.0 elap:             0.2
(Enter C:\Gaussian\G16W\l202.exe)
                        Input orientation:
---------------------------------------------------------------------
Center    Atomic    Atomic          Coordinates (Angstroms)
Number    Number    Type          X          Y          Z
---------------------------------------------------------------------
   1       7          0       5.715000 3.989000 1.700000
   2       7          0       1.550000 3.287000 1.700000
   3       6          0       4.328000 3.675000 1.700000
   4       6          0       3.790000 2.381000 1.700000
   5       1          0       4.443000 1.516000 1.700000
   6       6          0       2.405000 2.251000 1.700000
   7       1          0       1.950000 1.262000 1.700000
   8       6          0       3.453000 4.764000 1.700000
   9       1          0       3.850000 5.774000 1.700000
   10       6          0       2.080000 4.515000 1.700000
   11       1          0       1.373000 5.342000 1.700000
   12       7          0       6.473000 2.985000 1.700000
   13       7          0    10.638000 3.688000 1.700000
   14       6          0       7.860000 3.299000 1.700000
   15       6          0       8.399000 4.594000 1.700000
   16       1          0       7.745000 5.458000 1.700000
   17       6          0       9.783000 4.724000 1.700000
   18       1          0    10.238000 5.713000 1.700000
   19       6          0       8.736000 2.210000 1.700000
   20       1          0       8.338000 1.200000 1.700000
   21       6          0    10.109000 2.459000 1.700000
   22       1          0    10.816000 1.632000 1.700000
   23       -2          0    12.188000 0.000000 0.000000
   24       -2          0       0.000000 6.974000 0.000000
   25       -2          0       0.000000 0.000000 3.400000
---------------------------------------------------------------------
Lengths of translation vectors:    12.188000 6.974000 3.400000
  Angles of translation vectors:    90.000000 90.000000 90.000000
---------------------------------------------------------------------
                  Distance matrix (angstroms):
                  1       2       3       4       5
   1  N 0.000000
   2  N 4.223746 0.000000
   3  C 1.422099 2.804965 0.000000
   4  C 2.508244 2.416286 1.401385 0.000000
   5  H 2.780955 3.392033 2.162061 1.083805 0.000000
   6  C 3.738548 1.343250 2.392845 1.391088 2.166488
   7  H 4.648844 2.064128 3.387839 2.153546 2.505906
   8  C 2.391081 2.408929 1.396977 2.406711 3.395527
   9  H 2.581560 3.387502 2.152739 3.393530 4.299094
10  C 3.672860 1.337492 2.399813 2.734603 3.818085
11  H 4.547920 2.062609 3.392774 3.822226 4.905423
12  N 1.258006 4.932254 2.253248 2.750146 2.505766
13  N 4.932193 9.096843 6.310013 6.971611 6.564725
14  C 2.253248 6.310011 3.551957 4.172244 3.854216
15  C 2.751342 6.972593 4.173440 5.112754 5.012387
16  H 2.505766 6.564394 3.854216 5.010983 5.142234
17  C 4.133866 8.357467 5.554946 6.434726 6.229516
18  H 4.840424 9.020356 6.251523 7.258025 7.155196
19  C 3.505892 7.266259 4.645071 4.948955 4.348734
20  H 3.828662 7.101585 4.712295 4.698837 3.907797
21  C 4.652756 8.598957 5.907505 6.319481 5.743936
22  H 5.619221 9.412639 6.802058 7.065810 6.374056
23  TV 7.791139  11.263277 8.841675 8.893007 8.072997
24  TV 6.667942 4.345857 5.701314 6.192717 7.240167
25  TV 7.173796 4.012090 5.926821 4.787824 4.992845
                  6       7       8       9       10
   6  C 0.000000
   7  H 1.088644 0.000000
   8  C 2.722769 3.810907 0.000000
   9  H 3.807828 4.895727 1.085223 0.000000
10  C 2.287208 3.255597 1.395396 2.172091 0.000000
11  H 3.258728 4.120598 2.158815 2.514389 1.088016
12  N 4.133688 4.840068 3.505031 3.828662 4.651811
13  N 8.357467 9.020356 7.265122 7.101291 8.597866
14  C 5.554757 6.251197 4.644123 4.712295 5.906527
15  C 6.435657 7.258913 4.948921 4.699553 6.319494
16  H 6.229001 7.154610 4.347747 3.907797 5.742950
17  C 7.781427 8.563955 6.330126 6.025196 7.705835
18  H 8.563955 9.407568 6.851046 6.388291 8.245494
19  C 6.331133 6.851898 5.867964 6.047734 7.043817
20  H 6.025371 6.388301 6.046927 6.408090 7.081793
21  C 7.706807 8.246338 7.043817 7.082676 8.288062
22  H 8.433747 8.873717 8.001449 8.104401 9.199423
23  TV  10.181556  10.454630  10.093856  10.283546  11.200308
24  TV 5.566036 6.270522 4.438165 4.376357 3.641851
25  TV 3.706889 2.878393 6.124451 7.145039 5.253725
               11       12       13       14       15
11  H 0.000000
12  N 5.618314 0.000000
13  N 9.411479 4.223912 0.000000
14  C 6.801104 1.422099 2.805103 0.000000
15  C 7.065704 2.509653 2.415359 1.402692 0.000000
16  H 6.373056 2.780955 3.391511 2.162061 1.083611
17  C 8.432676 3.739013 1.343250 2.393440 1.390092
18  H 8.872760 4.649431 2.064128 3.388551 2.152692
19  C 8.001449 2.392027 2.408752 1.397604 2.407701
20  H 8.103542 2.581560 3.388236 2.152739 3.394548
21  C 9.199423 3.673850 1.338014 2.400750 2.735384
22  H 10.145657 4.548874 2.063691 3.393645 3.823001
23  TV  12.181592 6.667942 4.346705 5.701314 6.192847
24  TV 2.727371 7.791139  11.262985 8.841675 8.893683
25  TV 5.771663 7.328025  11.386764 8.692123 9.723067
               16       17       18       19       20
16  H 0.000000
17  C 2.166149 0.000000
18  H 2.506008 1.088644 0.000000
19  C 3.395819 2.723308 3.811432 0.000000
20  H 4.299094 3.808753 4.896649 1.085589 0.000000
21  C 3.818704 2.288340 3.256556 1.395396 2.172906
22  H 4.906049 3.259993 4.121728 2.158815 2.515374
23  TV 7.240167 5.566884 6.271433 4.437387 4.376357
24  TV 8.072997  10.181335  10.454509  10.094721  10.283546
25  TV 9.626255  10.996057  11.846730 9.170158 8.593733
               21       22       23       24       25
21  C 0.000000
22  H 1.088016 0.000000
23  TV 3.641280 2.726868 0.000000
24  TV  11.201210  12.182480  14.042223 0.000000
25  TV  10.541753  11.069746  12.653353 7.758652 0.000000
      Unit Cell Distance matrix (angstroms):
                  1       2       3       4       5
   1  N 0.000000
   2  N 4.223746 0.000000
   3  C 1.422099 2.804965 0.000000
   4  C 2.508244 2.416286 1.401385 0.000000
   5  H 2.780955 3.392033 2.162061 1.083805 0.000000
   6  C 3.738548 1.343250 2.392845 1.391088 2.166488
   7  H 4.648844 2.064128 3.387839 2.153546 2.505906
   8  C 2.391081 2.408929 1.396977 2.406711 3.395527
   9  H 2.581560 3.387502 2.152739 3.393530 4.299094
10  C 3.672860 1.337492 2.399813 2.734603 3.818085
11  H 4.547920 2.062609 3.392774 3.822226 4.905423
12  N 1.258006 4.932254 2.253248 2.750146 2.505766
13  N 4.932193 9.096843 6.310013 6.971611 6.564725
14  C 2.253248 6.310011 3.551957 4.172244 3.854216
15  C 2.751342 6.972593 4.173440 5.112754 5.012387
16  H 2.505766 6.564394 3.854216 5.010983 5.142234
17  C 4.133866 8.357467 5.554946 6.434726 6.229516
18  H 4.840424 9.020356 6.251523 7.258025 7.155196
19  C 3.505892 7.266259 4.645071 4.948955 4.348734
20  H 3.828662 7.101585 4.712295 4.698837 3.907797
21  C 4.652756 8.598957 5.907505 6.319481 5.743936
22  H 5.619221 9.412639 6.802058 7.065810 6.374056
                  6       7       8       9       10
   6  C 0.000000
   7  H 1.088644 0.000000
   8  C 2.722769 3.810907 0.000000
   9  H 3.807828 4.895727 1.085223 0.000000
10  C 2.287208 3.255597 1.395396 2.172091 0.000000
11  H 3.258728 4.120598 2.158815 2.514389 1.088016
12  N 4.133688 4.840068 3.505031 3.828662 4.651811
13  N 8.357467 9.020356 7.265122 7.101291 8.597866
14  C 5.554757 6.251197 4.644123 4.712295 5.906527
15  C 6.435657 7.258913 4.948921 4.699553 6.319494
16  H 6.229001 7.154610 4.347747 3.907797 5.742950
17  C 7.781427 8.563955 6.330126 6.025196 7.705835
18  H 8.563955 9.407568 6.851046 6.388291 8.245494
19  C 6.331133 6.851898 5.867964 6.047734 7.043817
20  H 6.025371 6.388301 6.046927 6.408090 7.081793
21  C 7.706807 8.246338 7.043817 7.082676 8.288062
22  H 8.433747 8.873717 8.001449 8.104401 9.199423
               11       12       13       14       15
11  H 0.000000
12  N 5.618314 0.000000
13  N 9.411479 4.223912 0.000000
14  C 6.801104 1.422099 2.805103 0.000000
15  C 7.065704 2.509653 2.415359 1.402692 0.000000
16  H 6.373056 2.780955 3.391511 2.162061 1.083611
17  C 8.432676 3.739013 1.343250 2.393440 1.390092
18  H 8.872760 4.649431 2.064128 3.388551 2.152692
19  C 8.001449 2.392027 2.408752 1.397604 2.407701
20  H 8.103542 2.581560 3.388236 2.152739 3.394548
21  C 9.199423 3.673850 1.338014 2.400750 2.735384
22  H 10.145657 4.548874 2.063691 3.393645 3.823001
               16       17       18       19       20
16  H 0.000000
17  C 2.166149 0.000000
18  H 2.506008 1.088644 0.000000
19  C 3.395819 2.723308 3.811432 0.000000
20  H 4.299094 3.808753 4.896649 1.085589 0.000000
21  C 3.818704 2.288340 3.256556 1.395396 2.172906
22  H 4.906049 3.259993 4.121728 2.158815 2.515374
               21       22
21  C 0.000000
22  H 1.088016 0.000000
Symmetry turned off by external request.
Symmetry turned off:
Cannot cope with ghost atoms or with translation vectors.
Stoichiometry C10H8N4
Framework group  C1[X(C10H8N4)]
Deg. of freedom 60
Full point group                C1    NOp 1
Leave Link  202 at Thu Feb 06 13:01:24 2025, MaxMem= 104857600 cpu:             0.0 elap:             0.0
(Enter C:\Gaussian\G16W\l301.exe)
Standard basis: 6-31G(d) (6D, 7F)
Ernie: Thresh=  0.10000D-02 Tol=  0.10000D-05 Strict=F.
226 basis functions, 424 primitive gaussians, 226 cartesian basis functions
48 alpha electrons    48 beta electrons
   nuclear repulsion energy    755.3707675781 Hartrees.
IExCor=  402 DFT=T Ex+Corr=B3LYP ExCW=0 ScaHFX=  0.200000
ScaDFX=  0.800000  0.720000  1.000000  0.810000 ScalE2=  1.000000  1.000000
IRadAn=    5 IRanWt=    -1 IRanGd=          0 ICorTp=0 IEmpDi=  4
NAtoms= 22 NActive= 22 NUniq= 22 SFac= 1.00D+00 NAtFMM= 60 NAOKFM=F Big=F
Integral buffers will be 131072 words long.
Raffenetti 2 integral format.
Two-electron integral symmetry is turned off.
Leave Link  301 at Thu Feb 06 13:01:24 2025, MaxMem= 104857600 cpu:             0.0 elap:             0.1
(Enter C:\Gaussian\G16W\l302.exe)
FOutLm=  100.00.
Periodicity:                         1             1             1
Max integer dimensions:             5             8             16
PBC vector 1 X= 23.0320 Y= 0.0000 Z= 0.0000
PBC vector 2 X=    0.0000 Y= 13.1789 Z= 0.0000
PBC vector 3 X=    0.0000 Y= 0.0000 Z= 6.4251
  Recp vector 1 X=    0.0434 Y= 0.0000 Z= 0.0000
  Recp vector 2 X=    0.0000 Y= 0.0759 Z= 0.0000
  Recp vector 3 X=    0.0000 Y= 0.0000 Z= 0.1556
Generated k point mesh (from -Pi to Pi):
K space mesh: X=    12 Y=    20 Z=    40
A half-cell shift: 0
Using k point mesh (from -Pi to Pi):
K space mesh: X=    12 Y=    20 Z=    40
A half-cell shift: 0
CountK=T Total number of k points:    0
CountK=T Total number of k points: 4804
NPDir=3 NMtPBC=  3979 NCelOv= 223 NCel= 3979 NClECP= 223 NCelD= 223
      NCelK= 3979 NCelE2=  3979 NClLst= 111 CellRange= 100.0.
Out-of-memory error in routine STVDrv-2 (IEnd=    204143624 MxCore=    104857600)
Use %mem=195MW to provide the minimum amount of memory required to complete this step.
Error termination via Lnk1e in C:\Gaussian\G16W\l302.exe at Thu Feb 06 13:01:25 2025.
Job cpu time:    0 days  0 hours  0 minutes  2.0 seconds.
Elapsed time:    0 days  0 hours  0 minutes  1.0 seconds.
File lengths (MBytes):  RWF=    6 Int=    0 D2E=    0 Chk=    1 Scr=    1
看网上说是内存原因，后又重新定义了内存
输入文件
%chk=new.chk
%mem=2GB
#p B3LYP/6-31G* nosymm

Generated by Multiwfn

  0  1
N    5.71500000 3.98900000 1.70000000
N    1.55000000 3.28700000 1.70000000
C    4.32800000 3.67500000 1.70000000
C    3.79000000 2.38100000 1.70000000
H    4.44300000 1.51600000 1.70000000
C    2.40500000 2.25100000 1.70000000
H    1.95000000 1.26200000 1.70000000
C    3.45300000 4.76400000 1.70000000
H    3.85000000 5.77400000 1.70000000
C    2.08000000 4.51500000 1.70000000
H    1.37300000 5.34200000 1.70000000
N    6.47300000 2.98500000 1.70000000
N    10.63800000 3.68800000 1.70000000
C    7.86000000 3.29900000 1.70000000
C    8.39900000 4.59400000 1.70000000
H    7.74500000 5.45800000 1.70000000
C    9.78300000 4.72400000 1.70000000
H    10.23800000 5.71300000 1.70000000
C    8.73600000 2.21000000 1.70000000
H    8.33800000 1.20000000 1.70000000
C    10.10900000 2.45900000 1.70000000
H    10.81600000 1.63200000 1.70000000
Tv 12.188000 0.000000 0.000000
Tv 0.000000 6.974000 0.000000
Tv 0.000000 0.000000 3.400000

输出文件
%chk=new.chk
%mem=2GB
----------------------
#p B3LYP/6-31G* nosymm
----------------------
1/38=1,172=1/1;
2/12=2,15=1,17=6,18=5,40=1/2;
3/5=1,6=6,7=1,11=2,25=1,30=1,74=-5/1,2,3;
4//1;
5/5=2,38=5/2;
6/7=2,8=2,9=2,10=2,28=1/1;
99/5=1,9=1/99;
Leave Link 1 at Thu Feb 06 13:14:42 2025, MaxMem= 268435456 cpu:             0.0 elap:             0.1
(Enter C:\Gaussian\G16W\l101.exe)
---------------------
Generated by Multiwfn
---------------------
Symbolic Z-matrix:
Charge =  0 Multiplicity = 1
N                   5.715    3.989    1.7
N                   1.55    3.287    1.7
C                   4.328    3.675    1.7
C                   3.79    2.381    1.7
H                   4.443    1.516    1.7
C                   2.405    2.251    1.7
H                   1.95    1.262    1.7
C                   3.453    4.764    1.7
H                   3.85    5.774    1.7
C                   2.08    4.515    1.7
H                   1.373    5.342    1.7
N                   6.473    2.985    1.7
N                   10.638 3.688    1.7
C                   7.86    3.299    1.7
C                   8.399    4.594    1.7
H                   7.745    5.458    1.7
C                   9.783    4.724    1.7
H                   10.238 5.713    1.7
C                   8.736    2.21    1.7
H                   8.338    1.2    1.7
C                   10.109 2.459    1.7
H                   10.816 1.632    1.7
Tv                   12.188 0.       0.
Tv                   0.       6.974    0.
Tv                   0.       0.       3.4

ITRead=  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
ITRead=  0  0  0  0  0
MicOpt= -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
MicOpt= -1 -1 -1 -1 -1
NAtoms=    25 NQM=    25 NQMF=    0 NMMI=    0 NMMIF=    0
            NMic=    0 NMicF=    0.
                  Isotopes and Nuclear Properties:
(Nuclear quadrupole moments (NQMom) in fm**2, nuclear magnetic moments (NMagM)
  in nuclear magnetons)

  Atom       1          2          3          4          5          6          7          8          9       10
IAtWgt=       14       14       12       12          1       12          1       12          1       12
AtmWgt=  14.0030740  14.0030740  12.0000000  12.0000000 1.0078250  12.0000000 1.0078250  12.0000000 1.0078250  12.0000000
NucSpn=          2          2          0          0          1          0          1          0          1          0
AtZEff= 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
NQMom= 2.0440000 2.0440000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
NMagM= 0.4037610 0.4037610 0.0000000 0.0000000 2.7928460 0.0000000 2.7928460 0.0000000 2.7928460 0.0000000
AtZNuc= 7.0000000 7.0000000 6.0000000 6.0000000 1.0000000 6.0000000 1.0000000 6.0000000 1.0000000 6.0000000

  Atom       11       12       13       14       15       16       17       18       19       20
IAtWgt=          1       14       14       12       12          1       12          1       12          1
AtmWgt= 1.0078250  14.0030740  14.0030740  12.0000000  12.0000000 1.0078250  12.0000000 1.0078250  12.0000000 1.0078250
NucSpn=          1          2          2          0          0          1          0          1          0          1
AtZEff= 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
NQMom= 0.0000000 2.0440000 2.0440000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
NMagM= 2.7928460 0.4037610 0.4037610 0.0000000 0.0000000 2.7928460 0.0000000 2.7928460 0.0000000 2.7928460
AtZNuc= 1.0000000 7.0000000 7.0000000 6.0000000 6.0000000 1.0000000 6.0000000 1.0000000 6.0000000 1.0000000

  Atom       21       22
IAtWgt=       12          1
AtmWgt=  12.0000000 1.0078250
NucSpn=          0          1
AtZEff= 0.0000000 0.0000000
NQMom= 0.0000000 0.0000000
NMagM= 0.0000000 2.7928460
AtZNuc= 6.0000000 1.0000000
Leave Link  101 at Thu Feb 06 13:14:42 2025, MaxMem= 268435456 cpu:             0.0 elap:             0.3
(Enter C:\Gaussian\G16W\l202.exe)
                        Input orientation:
---------------------------------------------------------------------
Center    Atomic    Atomic          Coordinates (Angstroms)
Number    Number    Type          X          Y          Z
---------------------------------------------------------------------
   1       7          0       5.715000 3.989000 1.700000
   2       7          0       1.550000 3.287000 1.700000
   3       6          0       4.328000 3.675000 1.700000
   4       6          0       3.790000 2.381000 1.700000
   5       1          0       4.443000 1.516000 1.700000
   6       6          0       2.405000 2.251000 1.700000
   7       1          0       1.950000 1.262000 1.700000
   8       6          0       3.453000 4.764000 1.700000
   9       1          0       3.850000 5.774000 1.700000
   10       6          0       2.080000 4.515000 1.700000
   11       1          0       1.373000 5.342000 1.700000
   12       7          0       6.473000 2.985000 1.700000
   13       7          0    10.638000 3.688000 1.700000
   14       6          0       7.860000 3.299000 1.700000
   15       6          0       8.399000 4.594000 1.700000
   16       1          0       7.745000 5.458000 1.700000
   17       6          0       9.783000 4.724000 1.700000
   18       1          0    10.238000 5.713000 1.700000
   19       6          0       8.736000 2.210000 1.700000
   20       1          0       8.338000 1.200000 1.700000
   21       6          0    10.109000 2.459000 1.700000
   22       1          0    10.816000 1.632000 1.700000
   23       -2          0    12.188000 0.000000 0.000000
   24       -2          0       0.000000 6.974000 0.000000
   25       -2          0       0.000000 0.000000 3.400000
---------------------------------------------------------------------
Lengths of translation vectors:    12.188000 6.974000 3.400000
  Angles of translation vectors:    90.000000 90.000000 90.000000
---------------------------------------------------------------------
                  Distance matrix (angstroms):
                  1       2       3       4       5
   1  N 0.000000
   2  N 4.223746 0.000000
   3  C 1.422099 2.804965 0.000000
   4  C 2.508244 2.416286 1.401385 0.000000
   5  H 2.780955 3.392033 2.162061 1.083805 0.000000
   6  C 3.738548 1.343250 2.392845 1.391088 2.166488
   7  H 4.648844 2.064128 3.387839 2.153546 2.505906
   8  C 2.391081 2.408929 1.396977 2.406711 3.395527
   9  H 2.581560 3.387502 2.152739 3.393530 4.299094
10  C 3.672860 1.337492 2.399813 2.734603 3.818085
11  H 4.547920 2.062609 3.392774 3.822226 4.905423
12  N 1.258006 4.932254 2.253248 2.750146 2.505766
13  N 4.932193 9.096843 6.310013 6.971611 6.564725
14  C 2.253248 6.310011 3.551957 4.172244 3.854216
15  C 2.751342 6.972593 4.173440 5.112754 5.012387
16  H 2.505766 6.564394 3.854216 5.010983 5.142234
17  C 4.133866 8.357467 5.554946 6.434726 6.229516
18  H 4.840424 9.020356 6.251523 7.258025 7.155196
19  C 3.505892 7.266259 4.645071 4.948955 4.348734
20  H 3.828662 7.101585 4.712295 4.698837 3.907797
21  C 4.652756 8.598957 5.907505 6.319481 5.743936
22  H 5.619221 9.412639 6.802058 7.065810 6.374056
23  TV 7.791139  11.263277 8.841675 8.893007 8.072997
24  TV 6.667942 4.345857 5.701314 6.192717 7.240167
25  TV 7.173796 4.012090 5.926821 4.787824 4.992845
                  6       7       8       9       10
   6  C 0.000000
   7  H 1.088644 0.000000
   8  C 2.722769 3.810907 0.000000
   9  H 3.807828 4.895727 1.085223 0.000000
10  C 2.287208 3.255597 1.395396 2.172091 0.000000
11  H 3.258728 4.120598 2.158815 2.514389 1.088016
12  N 4.133688 4.840068 3.505031 3.828662 4.651811
13  N 8.357467 9.020356 7.265122 7.101291 8.597866
14  C 5.554757 6.251197 4.644123 4.712295 5.906527
15  C 6.435657 7.258913 4.948921 4.699553 6.319494
16  H 6.229001 7.154610 4.347747 3.907797 5.742950
17  C 7.781427 8.563955 6.330126 6.025196 7.705835
18  H 8.563955 9.407568 6.851046 6.388291 8.245494
19  C 6.331133 6.851898 5.867964 6.047734 7.043817
20  H 6.025371 6.388301 6.046927 6.408090 7.081793
21  C 7.706807 8.246338 7.043817 7.082676 8.288062
22  H 8.433747 8.873717 8.001449 8.104401 9.199423
23  TV  10.181556  10.454630  10.093856  10.283546  11.200308
24  TV 5.566036 6.270522 4.438165 4.376357 3.641851
25  TV 3.706889 2.878393 6.124451 7.145039 5.253725
               11       12       13       14       15
11  H 0.000000
12  N 5.618314 0.000000
13  N 9.411479 4.223912 0.000000
14  C 6.801104 1.422099 2.805103 0.000000
15  C 7.065704 2.509653 2.415359 1.402692 0.000000
16  H 6.373056 2.780955 3.391511 2.162061 1.083611
17  C 8.432676 3.739013 1.343250 2.393440 1.390092
18  H 8.872760 4.649431 2.064128 3.388551 2.152692
19  C 8.001449 2.392027 2.408752 1.397604 2.407701
20  H 8.103542 2.581560 3.388236 2.152739 3.394548
21  C 9.199423 3.673850 1.338014 2.400750 2.735384
22  H 10.145657 4.548874 2.063691 3.393645 3.823001
23  TV  12.181592 6.667942 4.346705 5.701314 6.192847
24  TV 2.727371 7.791139  11.262985 8.841675 8.893683
25  TV 5.771663 7.328025  11.386764 8.692123 9.723067
               16       17       18       19       20
16  H 0.000000
17  C 2.166149 0.000000
18  H 2.506008 1.088644 0.000000
19  C 3.395819 2.723308 3.811432 0.000000
20  H 4.299094 3.808753 4.896649 1.085589 0.000000
21  C 3.818704 2.288340 3.256556 1.395396 2.172906
22  H 4.906049 3.259993 4.121728 2.158815 2.515374
23  TV 7.240167 5.566884 6.271433 4.437387 4.376357
24  TV 8.072997  10.181335  10.454509  10.094721  10.283546
25  TV 9.626255  10.996057  11.846730 9.170158 8.593733
               21       22       23       24       25
21  C 0.000000
22  H 1.088016 0.000000
23  TV 3.641280 2.726868 0.000000
24  TV  11.201210  12.182480  14.042223 0.000000
25  TV  10.541753  11.069746  12.653353 7.758652 0.000000
      Unit Cell Distance matrix (angstroms):
                  1       2       3       4       5
   1  N 0.000000
   2  N 4.223746 0.000000
   3  C 1.422099 2.804965 0.000000
   4  C 2.508244 2.416286 1.401385 0.000000
   5  H 2.780955 3.392033 2.162061 1.083805 0.000000
   6  C 3.738548 1.343250 2.392845 1.391088 2.166488
   7  H 4.648844 2.064128 3.387839 2.153546 2.505906
   8  C 2.391081 2.408929 1.396977 2.406711 3.395527
   9  H 2.581560 3.387502 2.152739 3.393530 4.299094
10  C 3.672860 1.337492 2.399813 2.734603 3.818085
11  H 4.547920 2.062609 3.392774 3.822226 4.905423
12  N 1.258006 4.932254 2.253248 2.750146 2.505766
13  N 4.932193 9.096843 6.310013 6.971611 6.564725
14  C 2.253248 6.310011 3.551957 4.172244 3.854216
15  C 2.751342 6.972593 4.173440 5.112754 5.012387
16  H 2.505766 6.564394 3.854216 5.010983 5.142234
17  C 4.133866 8.357467 5.554946 6.434726 6.229516
18  H 4.840424 9.020356 6.251523 7.258025 7.155196
19  C 3.505892 7.266259 4.645071 4.948955 4.348734
20  H 3.828662 7.101585 4.712295 4.698837 3.907797
21  C 4.652756 8.598957 5.907505 6.319481 5.743936
22  H 5.619221 9.412639 6.802058 7.065810 6.374056
                  6       7       8       9       10
   6  C 0.000000
   7  H 1.088644 0.000000
   8  C 2.722769 3.810907 0.000000
   9  H 3.807828 4.895727 1.085223 0.000000
10  C 2.287208 3.255597 1.395396 2.172091 0.000000
11  H 3.258728 4.120598 2.158815 2.514389 1.088016
12  N 4.133688 4.840068 3.505031 3.828662 4.651811
13  N 8.357467 9.020356 7.265122 7.101291 8.597866
14  C 5.554757 6.251197 4.644123 4.712295 5.906527
15  C 6.435657 7.258913 4.948921 4.699553 6.319494
16  H 6.229001 7.154610 4.347747 3.907797 5.742950
17  C 7.781427 8.563955 6.330126 6.025196 7.705835
18  H 8.563955 9.407568 6.851046 6.388291 8.245494
19  C 6.331133 6.851898 5.867964 6.047734 7.043817
20  H 6.025371 6.388301 6.046927 6.408090 7.081793
21  C 7.706807 8.246338 7.043817 7.082676 8.288062
22  H 8.433747 8.873717 8.001449 8.104401 9.199423
               11       12       13       14       15
11  H 0.000000
12  N 5.618314 0.000000
13  N 9.411479 4.223912 0.000000
14  C 6.801104 1.422099 2.805103 0.000000
15  C 7.065704 2.509653 2.415359 1.402692 0.000000
16  H 6.373056 2.780955 3.391511 2.162061 1.083611
17  C 8.432676 3.739013 1.343250 2.393440 1.390092
18  H 8.872760 4.649431 2.064128 3.388551 2.152692
19  C 8.001449 2.392027 2.408752 1.397604 2.407701
20  H 8.103542 2.581560 3.388236 2.152739 3.394548
21  C 9.199423 3.673850 1.338014 2.400750 2.735384
22  H 10.145657 4.548874 2.063691 3.393645 3.823001
               16       17       18       19       20
16  H 0.000000
17  C 2.166149 0.000000
18  H 2.506008 1.088644 0.000000
19  C 3.395819 2.723308 3.811432 0.000000
20  H 4.299094 3.808753 4.896649 1.085589 0.000000
21  C 3.818704 2.288340 3.256556 1.395396 2.172906
22  H 4.906049 3.259993 4.121728 2.158815 2.515374
               21       22
21  C 0.000000
22  H 1.088016 0.000000
Symmetry turned off by external request.
Symmetry turned off:
Cannot cope with ghost atoms or with translation vectors.
Stoichiometry C10H8N4
Framework group  C1[X(C10H8N4)]
Deg. of freedom 60
Full point group                C1    NOp 1
Leave Link  202 at Thu Feb 06 13:14:43 2025, MaxMem= 268435456 cpu:             0.0 elap:             0.0
(Enter C:\Gaussian\G16W\l301.exe)
Standard basis: 6-31G(d) (6D, 7F)
Ernie: Thresh=  0.10000D-02 Tol=  0.10000D-05 Strict=F.
226 basis functions, 424 primitive gaussians, 226 cartesian basis functions
48 alpha electrons    48 beta electrons
   nuclear repulsion energy    755.3707675781 Hartrees.
IExCor=  402 DFT=T Ex+Corr=B3LYP ExCW=0 ScaHFX=  0.200000
ScaDFX=  0.800000  0.720000  1.000000  0.810000 ScalE2=  1.000000  1.000000
IRadAn=    5 IRanWt=    -1 IRanGd=          0 ICorTp=0 IEmpDi=  4
NAtoms= 22 NActive= 22 NUniq= 22 SFac= 1.00D+00 NAtFMM= 60 NAOKFM=F Big=F
Integral buffers will be 131072 words long.
Raffenetti 2 integral format.
Two-electron integral symmetry is turned off.
Leave Link  301 at Thu Feb 06 13:14:43 2025, MaxMem= 268435456 cpu:             0.0 elap:             0.1
(Enter C:\Gaussian\G16W\l302.exe)
FOutLm=  100.00.
Periodicity:                         1             1             1
Max integer dimensions:             5             8             16
PBC vector 1 X= 23.0320 Y= 0.0000 Z= 0.0000
PBC vector 2 X=    0.0000 Y= 13.1789 Z= 0.0000
PBC vector 3 X=    0.0000 Y= 0.0000 Z= 6.4251
  Recp vector 1 X=    0.0434 Y= 0.0000 Z= 0.0000
  Recp vector 2 X=    0.0000 Y= 0.0759 Z= 0.0000
  Recp vector 3 X=    0.0000 Y= 0.0000 Z= 0.1556
Generated k point mesh (from -Pi to Pi):
K space mesh: X=    12 Y=    20 Z=    40
A half-cell shift: 0
Using k point mesh (from -Pi to Pi):
K space mesh: X=    12 Y=    20 Z=    40
A half-cell shift: 0
CountK=T Total number of k points:    0
CountK=T Total number of k points: 4804
NPDir=3 NMtPBC=  3979 NCelOv= 223 NCel= 3979 NClECP= 223 NCelD= 223
      NCelK= 3979 NCelE2=  3979 NClLst= 111 CellRange= 100.0.
One-electron integrals computed using PRISM.
NBasis= 226 RedAO= T EigKep=  9.33D-04  NBF= 226
NBsUse= 226 1.00D-06 EigRej= -1.00D+00 NBFU= 226
Precomputing XC quadrature grid using
IXCGrd= 4 IRadAn=          5 IRanWt=       -1 IRanGd=          0 AccXCQ= 0.00D+00.
RepCel:  MaxNCR=    223 NClRep=    223 NMtPBC= 3979.
Generated NRdTot=    0 NPtTot=          0 NUsed=          0 NTot=       32
NSgBfM=  2292  2237  2267  2285  2292 MxSgAt=  4906 MxSgA2= 469.
Leave Link  302 at Thu Feb 06 13:19:53 2025, MaxMem= 268435456 cpu:          310.0 elap:          310.5
(Enter C:\Gaussian\G16W\l303.exe)
DipDrv:  MaxL=1.
Not enough memory for dipole integrals, short by 646567447 words.
Leave Link  303 at Thu Feb 06 13:19:57 2025, MaxMem= 268435456 cpu:             3.0 elap:             2.6
(Enter C:\Gaussian\G16W\l401.exe)
Harris functional with IExCor=  402 and IRadAn=    5 diagonalized for initial guess.
RepCel:  MaxNCR=    223 NClRep=    223 NMtPBC= 3979.
HarFok:  IExCor=  402 AccDes= 0.00D+00 IRadAn=       5 IDoV= 2 UseB2=F ITyADJ=14
ICtDFT=  3500011 ScaDFX=  1.000000  1.000000  1.000000  1.000000
Not enough memory to run CalDSu, short by 232184415 words.
Error termination via Lnk1e in C:\Gaussian\G16W\l401.exe at Thu Feb 06 13:19:57 2025.
Job cpu time:    0 days  0 hours  5 minutes 15.0 seconds.
Elapsed time:    0 days  0 hours  5 minutes 14.1 seconds.
File lengths (MBytes):  RWF= 8573 Int=    0 D2E=    0 Chk=    1 Scr=    1
还是内存不足，但是我更多原子的体系能跑，也不显示内存不足。

Uus/pMeC6H4-/キ · 发表于 Post on 2025-2-6 13:35:24

输入输出文件应当作为帖子附件上传，而不是直接复制粘贴文本内容到帖子正文，现在这样过于冗长，且混在一起很难区分。

第一个问题，自行用文本编辑器修改输入文件，把元素符号后面那一长串括号删掉，把原子坐标后面的连接性关系表删掉，不然Gaussian会读到多余内容。第二第三个问题，把原子坐标最后Tv开头的三行删掉，不然Gaussian会当成周期性计算。诚然Multiwfn可以把pdb文件转化为gjf文件，但这绝对不意味着产生的Gaussian输入文件可以不经检查直接提交计算。

0.01 · 发表于 Post on 2025-2-6 14:13:10

Uus/pMeC6H4-/キ发表于 2025-2-6 13:35
输入输出文件应当作为帖子附件上传，而不是直接复制粘贴文本内容到帖子正文，现在这样过于冗长，且混在一起 ...

好的，谢谢

大志 · 发表于 Post on 2025-2-20 13:44:19

在GaussView中打开pdb后，不要直接更改，复制一下，创建新的窗口，重新粘贴上去，之后在新的窗口设置计算内容，可以快速解决这个问题。

0.01 · 发表于 Post on 2025-3-5 16:49:59

大志发表于 2025-2-20 13:44
在GaussView中打开pdb后，不要直接更改，复制一下，创建新的窗口，重新粘贴上去，之后在新的窗口设置计算内 ...

好的，谢谢

hphz · 发表于 Post on 2025-7-2 17:46:58

老师好，我也是一样的问题，但是我想问一下怎么把pdb转入gview里面的pdbname那一栏给删掉呢，我的原子数很多，一个一个删可太久了

Uus/pMeC6H4-/キ · 发表于 Post on 2025-7-2 18:15:24

hphz 发表于 2025-7-2 17:46
老师好，我也是一样的问题，但是我想问一下怎么把pdb转入gview里面的pdbname那一栏给删掉呢，我的原子数很 ...

用GaussView打开.pdb文件后，先打开Calculate - Gaussian Calculation Setup窗口（鼠标去菜单栏点击或者直接键盘ctrl+G快捷键），切换到General栏并把右侧Write PDB Data（以及Write Connectivity）前面的对勾去掉，点Retain退出窗口，再保存结构为.gjf文件。

如果想在已经保存了的.gjf文件上修改，可以用ultraedit或VSCode等文本编辑器的列编辑模式处理，比如在VSCode里把光标放到合适位置后，用ctrl+alt+↑/↓键产生垂直多行的光标，再用shift+←/→键选择文本，最后del一键删除。

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[Gaussian/gview] 生成pdb格式的文件在gview里转换为gjf格式，Gaussian计算一直报错

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