基于amber的MCPB.py构建含金属离子蛋白的力场参数

Joysharing

Joysharing 发表于 2024-11-18 02:12
想请问一下各位老师，最后一步使用parmed将amber文件转换为gromacs文件出现这种情况怎么办呢，下面是报错文 ...

继续求问，感谢各位老师

zxczxc

你好，我在进行到
MCPB.py -i 7RB1.in -s 3
一直出现这个错误是怎么回事
*======================RESP Charge fitting=======================*
*                                                                *
******************************************************************
***Generating the 1st stage resp charge fitting input file...
***Generating the 2nd stage resp charge fitting input file...
***Doing the RESP charge fiting...
Traceback (most recent call last):
  File "/opt/amber22/bin/MCPB.py", line 692, in <module>
    resp_fitting(stpdbf, lgpdbf, stfpf, lgfpf, mklogf, ionids, ff_choice,
  File "/opt/amber22/lib/python3.10/site-packages/pymsmt/mcpb/resp_fitting.py", line 442, in resp_fitting
    get_esp_from_gau(mklogf, espf)
  File "/opt/amber22/lib/python3.10/site-packages/pymsmt/mol/gauio.py", line 663, in get_esp_from_gau
    esp = float(line[-1])
ValueError: could not convert string to float: 'Z'

其中，我的7RB1.in文件如下
# input file
# 7RB1.in
software_version g09
original_pdb 7RB1_fixed_H.pdb
group_name 7RB1
cut_off 2.8
ion_ids 13060
ion_mol2files MG.mol2
naa_mol2files LG1.mol2 LG2.mol2 WA1.mol2 WA2.mol2 WA3.mol2
frcmod_files LG1.frcmod LG2.frcmod frcmod.tip3p
large_opt 1

万分感谢

zxczxc

你好，我在进行到
MCPB.py -i 7RB1.in -s 3
一直出现这个错误是怎么回事
*======================RESP Charge fitting=======================*
*                                                                *
******************************************************************
***Generating the 1st stage resp charge fitting input file...
***Generating the 2nd stage resp charge fitting input file...
***Doing the RESP charge fiting...
Traceback (most recent call last):
  File "/opt/amber22/bin/MCPB.py", line 692, in <module>
    resp_fitting(stpdbf, lgpdbf, stfpf, lgfpf, mklogf, ionids, ff_choice,
  File "/opt/amber22/lib/python3.10/site-packages/pymsmt/mcpb/resp_fitting.py", line 442, in resp_fitting
    get_esp_from_gau(mklogf, espf)
  File "/opt/amber22/lib/python3.10/site-packages/pymsmt/mol/gauio.py", line 663, in get_esp_from_gau
    esp = float(line[-1])
ValueError: could not convert string to float: 'Z'

其中，我的7RB1.in文件如下
# input file
# 7RB1.in
software_version g09
original_pdb 7RB1_fixed_H.pdb
group_name 7RB1
cut_off 2.8
ion_ids 13060
ion_mol2files MG.mol2
naa_mol2files LG1.mol2 LG2.mol2 WA1.mol2 WA2.mol2 WA3.mol2
frcmod_files LG1.frcmod LG2.frcmod frcmod.tip3p
large_opt 1

万分感谢

云隐i

kepler_ye 发表于 2022-3-22 11:49
**** 作者被禁止或删除 内容自动屏蔽 ****

你好，请问如何解决了

小老弟

你好，我在进行”MCPB.py -i APOBECT2.in -s 1“时，出现以下报错，请问是什么原因，该如何解决呢？
Residue 25-GLU
Residue 63-HIP
Residue 93-CYM
Residue 96-CYM
Residue 249-HIP
Residue 279-CYM
Residue 282-CYM
Residue 396-GLU
Residue 434-HIP
Residue 464-CYM
Residue 467-CYM
Residue 619-HIP
Residue 649-CYM
Residue 652-CYM
Residue 740-ZN
Residue 741-ZN
Residue 742-ZN
Residue 743-ZN
***The small model contains the following residues:
[25, 63, 93, 96, 249, 279, 282, 396, 434, 464, 467, 619, 649, 652, 740, 741, 742, 743]
***The large model contains the following residues:
[24, 25, 26, 62, 63, 64, 92, 93, 94, 95, 96, 97, 248, 249, 250, 278, 279, 280, 281, 282, 283, 395, 396, 397, 433, 434, 435, 463, 464, 465, 466, 467, 468, 618, 619, 620, 648, 649, 650, 651, 652, 653, 740, 741, 742, 743]
******************************************************************
*                                                                *
*=======================Building models==========================*
*                                                                *
******************************************************************
***Creating the small model...
It contains the residue 25-GLU as sidechain coordinated.
It contains the residue 63-HIP as sidechain coordinated.
It contains the residue 93-CYM as sidechain coordinated.
It contains the residue 96-CYM as sidechain coordinated.
It contains the residue 249-HIP as sidechain coordinated.
It contains the residue 279-CYM as sidechain coordinated.
It contains the residue 282-CYM as sidechain coordinated.
It contains the residue 396-GLU as sidechain coordinated.
It contains the residue 434-HIP as sidechain coordinated.
It contains the residue 464-CYM as sidechain coordinated.
It contains the residue 467-CYM as sidechain coordinated.
It contains the residue 619-HIP as sidechain coordinated.
It contains the residue 649-CYM as sidechain coordinated.
It contains the residue 652-CYM as sidechain coordinated.
It contains the residue 740-ZN as normal.
It contains the residue 741-ZN as normal.
It contains the residue 742-ZN as normal.
It contains the residue 743-ZN as normal.
Totally there are 158 atoms in the small model.
Totally there are 688 electrons in the small model.
***Creating the standard model...
It contains the residue 25-GLU as normal.
Traceback (most recent call last):
  File "/public7/zhangao/biosoft/ambertools/bin/MCPB.py", line 662, in <module>
    gene_model_files(orpdbf, ionids, addres, addbpairs, gname, ff_choice,
    ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        premol2fs, cutoff, watermodel, 2, largeopt, sqmopt, smchg, smspin,
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        addred, lgchg, lgspin)
        ^^^^^^^^^^^^^^^^^^^^^^
  File "/public0/zhangao/biosoft/ambertools/lib/python3.13/site-packages/pymsmt/mcpb/gene_model_files.py", line 1906, in gene_model_files
    build_standard_model(mol, reslist, cutoff, msresids, outf, ionids,
    ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
                         bdedatms, addbpairs, libdict, autoattyp)
                         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/public0/zhangao/biosoft/ambertools/lib/python3.13/site-packages/pymsmt/mcpb/gene_model_files.py", line 1471, in build_standard_model
    attype = libdict[resname + '-' + atname][0]
             ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^
KeyError: 'GLU-HB1'