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标题: Amber20 能量最小化计算输出的rst文件转化成pdb文件，缺少原子坐标 [打印本页]

作者
Author: sxwen 时间: 2023-10-16 20:25
标题: Amber20 能量最小化计算输出的rst文件转化成pdb文件，缺少原子坐标
各位老师和同学好：
我有一个蛋白（nlrp3）,我们自己设计了一个化合物（st4）,我们想研究st4与nlrp3相互作用关系，我们使用moe将st4的C和nlrp3的S连接后，导出为pdb结构，然后按照Amber教程使用Antechamber处理小分子st4（将CYS改成CYP，将ST4也改成CYP，作为一个整体处理，因为分开处理时缺少c-sh-c信息），得到了nlrp3.prmtop和nlrp3.inpcrd文件，使用命令ambpdb -p nlrp3.prmtop < nlrp3.inpcrd > nlrp3_ambpdb_leap.pdb，生成了nlrp3_ambpdb_leap.pdb（见附件），将其导入pymol后检查并没有问题，只是CYP“残基”上下多了两个TER，如下：
ATOM 2481  O SER 149    -5.850 -12.074 -12.570  1.00  0.00
TER
ATOM 2482  N CYP 150    -7.662 -12.808 -11.462  1.00  0.00
ATOM 2483  CA  CYP 150    -7.000 -13.292 -10.238  1.00  0.00
ATOM 2484  CB  CYP 150    -7.754 -12.931  -8.954  1.00  0.00
ATOM 2485  SG  CYP 150    -7.620 -11.129  -8.594  1.00  0.00
ATOM 2486  C CYP 150    -6.544 -14.760 -10.228  1.00  0.00
ATOM 2487  O CYP 150    -6.039 -15.224  -9.207  1.00  0.00
ATOM 2488  H7  CYP 150    -8.575 -13.209 -11.528  1.00  0.00
ATOM 2489  H8  CYP 150    -7.122 -13.075 -12.261  1.00  0.00
ATOM 2490  H9  CYP 150    -6.087 -12.891 -10.172  1.00  0.00
ATOM 2491  H10 CYP 150    -7.552 -13.608  -8.247  1.00  0.00
ATOM 2492  H11 CYP 150    -8.737 -12.923  -9.136  1.00  0.00
ATOM 2493  H12 CYP 150    -5.756 -14.869 -10.836  1.00  0.00
ATOM 2494  C1  CYP 150    -6.079 -10.508  -9.452  1.00  0.00
ATOM 2495  C2  CYP 150    -3.691 -10.220 -11.048  1.00  0.00
ATOM 2496  C3  CYP 150    -3.752 -11.531 -10.212  1.00  0.00
ATOM 2497  O1  CYP 150    -4.081 -12.680 -10.923  1.00  0.00
ATOM 2498  C4  CYP 150    -4.666 -11.127  -9.022  1.00  0.00
ATOM 2499  C5  CYP 150    -3.771  -9.965  -8.677  1.00  0.00
ATOM 2500  C6  CYP 150    -3.017  -9.399  -9.934  1.00  0.00
ATOM 2501  C7  CYP 150    -3.230  -7.859  -9.876  1.00  0.00
ATOM 2502  C8  CYP 150    -2.086  -7.302  -8.996  1.00  0.00
ATOM 2503  C9  CYP 150    -0.664  -7.473  -9.587  1.00  0.00
ATOM 2504  C10 CYP 150    -0.543  -8.696 -10.544  1.00  0.00
ATOM 2505  C11 CYP 150    0.922  -9.178 -10.730  1.00  0.00
ATOM 2506  C12 CYP 150    1.927  -8.017 -10.651  1.00  0.00
ATOM 2507  C13 CYP 150    -0.925  -8.283 -12.006  1.00  0.00
ATOM 2508  C14 CYP 150    0.504  -7.325  -8.555  1.00  0.00
ATOM 2509  C15 CYP 150    1.830  -7.203  -9.359  1.00  0.00
ATOM 2510  C16 CYP 150    0.526  -8.522  -7.561  1.00  0.00
ATOM 2511  O2  CYP 150    -3.497  -9.720  -7.537  1.00  0.00
ATOM 2512  C17 CYP 150    -2.355 -12.055  -9.691  1.00  0.00
ATOM 2513  C18 CYP 150    -1.277 -11.041  -9.223  1.00  0.00
ATOM 2514  C19 CYP 150    -1.503  -9.856 -10.163  1.00  0.00
ATOM 2515  C20 CYP 150    0.466  -6.038  -7.707  1.00  0.00
ATOM 2516  O3  CYP 150    0.648  -6.025  -6.491  1.00  0.00
ATOM 2517  O4  CYP 150    0.365  -4.882  -8.384  1.00  0.00
ATOM 2518  H25 CYP 150    -5.985  -9.525  -9.299  1.00  0.00
ATOM 2519  H26 CYP 150    -6.149 -10.688 -10.433  1.00  0.00
ATOM 2520  H27 CYP 150    -4.618  -9.944 -11.303  1.00  0.00
ATOM 2521  H28 CYP 150    -3.150 -10.374 -11.875  1.00  0.00
ATOM 2522  H29 CYP 150    -3.416 -12.821 -11.656  1.00  0.00
ATOM 2523  H30 CYP 150    -4.783 -11.696  -8.208  1.00  0.00
ATOM 2524  H32 CYP 150    -4.124  -7.661  -9.473  1.00  0.00
ATOM 2525  H33 CYP 150    -3.190  -7.481 -10.801  1.00  0.00
ATOM 2526  H34 CYP 150    -2.076  -7.781  -8.119  1.00  0.00
ATOM 2527  H35 CYP 150    -2.231  -6.324  -8.840  1.00  0.00
ATOM 2528  H36 CYP 150    -0.425  -6.662 -10.121  1.00  0.00
ATOM 2529  H37 CYP 150    1.019  -9.612 -11.626  1.00  0.00
ATOM 2530  H38 CYP 150    1.150  -9.837 -10.014  1.00  0.00
ATOM 2531  H39 CYP 150    1.777  -7.393 -11.418  1.00  0.00
ATOM 2532  H40 CYP 150    2.858  -8.379 -10.692  1.00  0.00
ATOM 2533  H41 CYP 150    -1.867  -7.948 -12.023  1.00  0.00
ATOM 2534  H42 CYP 150    -0.843  -9.077 -12.609  1.00  0.00
ATOM 2535  H43 CYP 150    -0.309  -7.560 -12.321  1.00  0.00
ATOM 2536  H44 CYP 150    1.960  -6.233  -9.566  1.00  0.00
ATOM 2537  H45 CYP 150    2.538  -7.504  -8.721  1.00  0.00
ATOM 2538  H46 CYP 150    0.662  -9.374  -8.068  1.00  0.00
ATOM 2539  H47 CYP 150    -0.342  -8.562  -7.068  1.00  0.00
ATOM 2540  H48 CYP 150    1.274  -8.400  -6.909  1.00  0.00
ATOM 2541  H50 CYP 150    -1.903 -12.576 -10.415  1.00  0.00
ATOM 2542  H51 CYP 150    -2.496 -12.645  -8.895  1.00  0.00
ATOM 2543  H52 CYP 150    -0.372 -11.463  -9.283  1.00  0.00
ATOM 2544  H53 CYP 150    -1.458 -10.774  -8.276  1.00  0.00
ATOM 2545  H54 CYP 150    -1.722 -10.194 -11.079  1.00  0.00
ATOM 2546  H56 CYP 150    0.199  -5.224  -6.095  1.00  0.00
TER
ATOM 2547  N CYS 151    -6.695 -15.498 -11.328  1.00  0.00

紧着这，使用生成的nlrp3.prmtop和nlrp3.inpcrd文件进行能量最小化，输入如下(min.in)：
Initial minimisation of NLRP3-ST4 complex
&cntrl
  imin=1, maxcyc=200, ncyc=50,
  cut=16, ntb=0, igb=1,
  ntr=1, restraint_wt=10.0, restraintmask='!:WAT & !@H=',
&end

运行命令
mpirun -n 8 sander.MPI -O -p nlrp3.prmtop -c nlrp3.inpcrd -ref nlrp3.inpcrd -i min.in -o min.out -r min.rst &
cpptraj -p nlrp3.prmtop -y min.rst -x min.rst7
查看min.rst7文件，内容如下：
Cpptraj Generated Restart
76006  0.0000000E+00
      -nan       -nan       -nan       -nan       -nan       -nan
      -nan       -nan       -nan       -nan       -nan       -nan
      -nan       -nan       -nan       -nan       -nan       -nan
   .....
生成pdb内容：
ATOM    1  N GLY    1       nan    nan    nan  1.00  0.00          N
ATOM    2  H1  GLY    1       nan    nan    nan  1.00  0.00          H
ATOM    3  H2  GLY    1       nan    nan    nan  1.00  0.00          H
ATOM    4  H3  GLY    1       nan    nan    nan  1.00  0.00          H
ATOM    5  CA  GLY    1       nan    nan    nan  1.00  0.00          C
ATOM    6  HA2 GLY    1       nan    nan    nan  1.00  0.00          H
ATOM    7  HA3 GLY    1       nan    nan    nan  1.00  0.00          H

......
查看min.ou文件：
--------------------------------------------------------------------------------
4.  RESULTS
--------------------------------------------------------------------------------
NSTEP    ENERGY       RMS          GMAX       NAME NUMBER
   1             NaN          NaN    1.0878E+02    HG3    953
BOND =    607.6586  ANGLE =    1779.2615  DIHED    =    6822.3541
VDWAALS =          NaN  EEL    =    Infinity  EGB       =          NaN
1-4 VDW =    2240.6465  1-4 EEL = 20819.8067  RESTRAINT  =       0.0000
NSTEP    ENERGY       RMS          GMAX       NAME NUMBER
   50             NaN          NaN    0.0000E+00    N          1
BOND =          NaN  ANGLE =          NaN  DIHED    =          NaN
VDWAALS =       0.0000  EEL    =       0.0000  EGB       = -3709683.6084
1-4 VDW =          NaN  1-4 EEL =          NaN  RESTRAINT  =          NaN
EAMBER  =          NaN
.....

请问大家，这是哪里出错啊？
另外，最小化中将ntb=0, igb=1，改为ntb=1，将出现报错
$ sander -O -i min.in -o nlrp3_min_.out -p nlrp3.prmtop -c nlrp3.inpcrd -ref nlrp3.inpcrd -r nlrp3_min_.crd
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image             PC             Routine          Line       Source
sander          0000000000DB8E14  for__signal_handl    Unknown  Unknown
libpthread-2.17.s  00002B2E75D175F0  Unknown             Unknown  Unknown
sander          00000000007C2A80  short_ene_          Unknown  Unknown
sander          00000000007B7EDB  get_nb_energy_       Unknown  Unknown
sander          00000000007781ED  ewald_force_       Unknown  Unknown
sander          00000000006892DC  force_             Unknown  Unknown
sander          0000000000703286  runmin_             Unknown  Unknown
sander          00000000006EC37F  sander_             Unknown  Unknown
sander          00000000006E3116  MAIN__             Unknown  Unknown
sander          0000000000465B5E  main                Unknown  Unknown
libc-2.17.so    00002B2E77822505  __libc_start_main    Unknown  Unknown
sander          0000000000465A69  Unknown             Unknown  Unknown

这又是为什么呢?
(, 下载次数 Times of downloads: 1)

作者
Author: Serious 时间: 2023-10-17 09:52
1）ntb参数是设定什么的？先仔细看看手册；
2）所给信息太少，假设处理后的top和crd文件没有问题，按照min.out先看结构受力大的原子；其次修改min.in，调小输出步长，修改restraintmask（依我看，原先设定固定了蛋白除氢外所有原子，那突变的非标准氨基酸残基呢？），依据min.out看看多个结构，慢慢排除问题吧；
3）附件只有min.out；

作者
Author: sxwen 时间: 2023-10-17 17:14

Serious 发表于 2023-10-17 09:52
1）ntb参数是设定什么的？先仔细看看手册；
2）所给信息太少，假设处理后的top和crd文件没有问题，按照min ...

谢谢老师的回复，经过检查我发现是结构的问题，在生成inpcrd和prmtop文件时，CYP和ST4都被添加原子形成了两个一样的CYP-ST4，使用在生成inpcrd和prmtop文件时同时保存的pdb文件，只保留原CYP处的CYP-ST4，再次使用tleap生成deleted.inpcrd和deleted.prmtop文件，这时就没有上述问题了，然后min.in文件内容如下：
Initial minimisation of NLRP3-ST4 complex
&cntrl
  imin=1, maxcyc=2500, ncyc=1000,
  cut=10, ntb=1,ntr=0,
&end
出现了以下报错：
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image             PC             Routine          Line       Source
pmemd.MPI       00000000008305C4  for__signal_handl    Unknown  Unknown
libpthread-2.17.s  00002AC208D205D0  Unknown             Unknown  Unknown
pmemd.MPI       00000000005763A3  nb_exclusions_mod    Unknown  Unknown
pmemd.MPI       000000000055143A  pme_force_mod_mp_    Unknown  Unknown
pmemd.MPI       00000000005BFD05  runmin_mod_mp_run    Unknown  Unknown
pmemd.MPI       00000000006103FA  MAIN__             Unknown  Unknown
pmemd.MPI       000000000044259E  main                Unknown  Unknown
libc-2.17.so    00002AC20B1913D5  __libc_start_main    Unknown  Unknown
pmemd.MPI       00000000004424A9  Unknown             Unknown  Unknown

检查min.out文件发现EEL值有的有，有的没有，
......
NSTEP    ENERGY       RMS          GMAX       NAME NUMBER
100    -2.6104E+05    2.0790E+02    5.7064E+04    O3B    9128

BOND = 14320.3109  ANGLE =    1499.9476  DIHED    =    2549.2848
UB    =       0.0000  IMP    =       0.0000  CMAP    =    572.3873
VDWAALS = 18427.6997  EEL    =  -318027.5642  HBOND    =       0.0000
1-4 VDW =    1925.1241  1-4 EEL = 17693.2580  RESTRAINT  =       0.0000

NSTEP    ENERGY       RMS          GMAX       NAME NUMBER
150    -3.0174E+07    2.2747E+10    6.2281E+12    H51    9143

BOND = 14320.3621  ANGLE =    1499.6437  DIHED    =    2549.2993
UB    =       0.0000  IMP    =       0.0000  CMAP    =    572.3870
VDWAALS = 18427.6636  EEL    =  -318028.2544  HBOND    =       0.0000
1-4 VDW =    1925.1186  1-4 EEL = *************  RESTRAINT  =       0.0000

NSTEP    ENERGY       RMS          GMAX       NAME NUMBER
200    -8.0203E+07    1.6245E+11    4.4478E+13    H51    9143

BOND = 14320.3621  ANGLE =    1499.6437  DIHED    =    2549.2993
UB    =       0.0000  IMP    =       0.0000  CMAP    =    572.3870
VDWAALS = 18427.6636  EEL    =  -318028.2544  HBOND    =       0.0000
1-4 VDW =    1925.1186  1-4 EEL = *************  RESTRAINT  =       0.0000

NSTEP    ENERGY       RMS          GMAX       NAME NUMBER
250    -7.3479E+06    1.2776E+09    3.4980E+11    H51    9143

BOND = 14320.3621  ANGLE =    1499.6436  DIHED    =    2549.2993
UB    =       0.0000  IMP    =       0.0000  CMAP    =    572.3870
VDWAALS = 18427.6636  EEL    =  -318028.2545  HBOND    =       0.0000
1-4 VDW =    1925.1186  1-4 EEL = -7069156.6254  RESTRAINT  =       0.0000

NSTEP    ENERGY       RMS          GMAX       NAME NUMBER
300    -3.2460E+07    2.6357E+10    7.2164E+12    H51    9143

BOND = 14320.3621  ANGLE =    1499.6437  DIHED    =    2549.2993
UB    =       0.0000  IMP    =       0.0000  CMAP    =    572.3870
VDWAALS = 18427.6636  EEL    =  -318028.2544  HBOND    =       0.0000
1-4 VDW =    1925.1186  1-4 EEL = *************  RESTRAINT  =       0.0000

NSTEP    ENERGY       RMS          GMAX       NAME NUMBER
350    -8.0203E+07    1.6245E+11    4.4478E+13    H51    9143

BOND = 14320.3621  ANGLE =    1499.6437  DIHED    =    2549.2993
UB    =       0.0000  IMP    =       0.0000  CMAP    =    572.3870
VDWAALS = 18427.6636  EEL    =  -318028.2544  HBOND    =       0.0000
1-4 VDW =    1925.1186  1-4 EEL = *************  RESTRAINT  =       0.0000

NSTEP    ENERGY       RMS          GMAX       NAME NUMBER
400    -7.3479E+06    1.2776E+09    3.4980E+11    H51    9143

BOND = 14320.3621  ANGLE =    1499.6436  DIHED    =    2549.2993
UB    =       0.0000  IMP    =       0.0000  CMAP    =    572.3870
VDWAALS = 18427.6636  EEL    =  -318028.2545  HBOND    =       0.0000
1-4 VDW =    1925.1186  1-4 EEL = -7069156.6347  RESTRAINT  =       0.0000
......

请问老师，这是什么原因造成的啊，应该从哪些方面入手解决呢？我的小分子ADP和CYP-ST4都是使用
Antechamber -c bbc计算的电荷

作者
Author: Serious 时间: 2023-10-19 10:45

sxwen 发表于 2023-10-17 17:14
谢谢老师的回复，经过检查我发现是结构的问题，在生成inpcrd和prmtop文件时，CYP和ST4都被添加原子形成了 ...

1）小分子力场参数有问题；先看看H51因为什么受力过大，再检查是不是缺了什么力场参数；

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