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本帖最后由 ecolitib 于 2021-12-30 10:16 编辑
各位老师,有一个蛋白复合体含金属离子、NADP和底物小分子,index如下。把蛋白、金属离子和NADP分成一组(26)作为受体,想用gmx_mmpbsa计算底物小分子的结合自由能。命令:mpirun -np 8 gmx_MMPBSA MPI -O -i mmpbsa.in -cs ../md.tpr -ci ../mmpbsa_index.ndx -cg 26 15 -ct ../md.xtc -lm ../UNK.acpype/UNK_bcc_gaff.mol2
mmpbsa.in内容:
&general
startframe=2000, endframe=5000, verbose=2, interval=60,
forcefields="oldff/leaprc.ff14SB, leaprc.gaff"
temperature = 298.15,
/
&gb
igb=5, saltcon=0.150,
/
报错:
The unperturbed charge of the unit (-5.000000) is not zero.
FATAL: Atom .R<NAP 706>.A<O3X 48> does not have a type.
FATAL: Atom .R<NAP 706>.A<O2X 47> does not have a type.
FATAL: Atom .R<NAP 706>.A<O1X 46> does not have a type.
FATAL: Atom .R<NAP 706>.A<P2B 45> does not have a type.
......
/miniconda3/envs/AmberTools/bin/teLeap: Fatal Error!
Failed to generate parameters
请问是哪里错了,如何解决?
0 System : 155088 atoms
1 Protein : 10599 atoms
2 Protein-H : 5261 atoms
3 C-alpha : 702 atoms
4 Backbone : 2106 atoms
5 MainChain : 2810 atoms
6 MainChain+Cb : 3426 atoms
7 MainChain+H : 3472 atoms
8 SideChain : 7127 atoms
9 SideChain-H : 2451 atoms
10 Prot-Masses : 10599 atoms
11 non-Protein : 144489 atoms
12 Ion : 10 atoms
13 ZN : 1 atoms
14 NAP : 74 atoms
15 UNK : 12 atoms
16 NA : 9 atoms
17 Other : 86 atoms
18 ZN : 1 atoms
19 NAP : 74 atoms
20 UNK : 12 atoms
21 NA : 9 atoms
22 Water : 144393 atoms
23 SOL : 144393 atoms
24 non-Water : 10695 atoms
25 Water_and_ions : 144403 atoms
26 Protein_ZN_NAP : 10674 atoms
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