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Amber MD生成体系的力场参数文件不成功

作者 shuigezhi
来源: 小木虫 200 4 举报帖子
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如下所示,在Amber MD生成体系的力场参数文件不成功
> saveamberparm complex NIT101-SUB.prmtop NIT101-SUB.inpcrd
Checking Unit.

Warning: There is a bond of 3.731338 angstroms between:

Warning: The unperturbed charge of the unit (-9.997002) is not zero.

Note: Ignoring the warnings from Unit Checking.

Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.

Error: Could not find angle parameter: n1 - c3 - hc

Error: Could not find angle parameter: n1 - c3 - hc

Error: Could not find angle parameter: n1 - c3 - hc
Building proper torsion parameters.

Note: 1-4: angle 4447 4448 duplicates bond ('triangular' bond) or angle ('square' bond)


Note: 1-4: angle 4447 4455 duplicates bond ('triangular' bond) or angle ('square' bond)


Note: 1-4: angle 4447 4456 duplicates bond ('triangular' bond) or angle ('square' bond)


Note: 1-4: angle 4447 4457 duplicates bond ('triangular' bond) or angle ('square' bond)


Note: 1-4: angle 4447 4448 duplicates bond ('triangular' bond) or angle ('square' bond)


Note: 1-4: angle 4447 4455 duplicates bond ('triangular' bond) or angle ('square' bond)


Note: 1-4: angle 4447 4456 duplicates bond ('triangular' bond) or angle ('square' bond)


Note: 1-4: angle 4447 4457 duplicates bond ('triangular' bond) or angle ('square' bond)


Note: 1-4: angle 4445 4447 duplicates bond ('triangular' bond) or angle ('square' bond)


Note: 1-4: angle 4445 4447 duplicates bond ('triangular' bond) or angle ('square' bond)


Error:  ** No torsion terms for  c3-n1-c1-c3
Building improper torsion parameters.
** Warning: No sp2 improper torsion term for  C*-CN-CB-CA
        atoms are: CG CE2 CD2 CE3
** Warning: No sp2 improper torsion term for  NA-CA-CN-CB
        atoms are: NE1 CZ2 CE2 CD2
** Warning: No sp2 improper torsion term for  C*-CN-CB-CA
        atoms are: CG CE2 CD2 CE3
** Warning: No sp2 improper torsion term for  NA-CA-CN-CB
        atoms are: NE1 CZ2 CE2 CD2
** Warning: No sp2 improper torsion term for  C*-CN-CB-CA
        atoms are: CG CE2 CD2 CE3
** Warning: No sp2 improper torsion term for  NA-CA-CN-CB
        atoms are: NE1 CZ2 CE2 CD2
** Warning: No sp2 improper torsion term for  C*-CN-CB-CA
        atoms are: CG CE2 CD2 CE3
** Warning: No sp2 improper torsion term for  NA-CA-CN-CB
        atoms are: NE1 CZ2 CE2 CD2
** Warning: No sp2 improper torsion term for  C*-CN-CB-CA
        atoms are: CG CE2 CD2 CE3
** Warning: No sp2 improper torsion term for  NA-CA-CN-CB
        atoms are: NE1 CZ2 CE2 CD2
** Warning: No sp2 improper torsion term for  C*-CN-CB-CA
        atoms are: CG CE2 CD2 CE3
** Warning: No sp2 improper torsion term for  NA-CA-CN-CB
        atoms are: NE1 CZ2 CE2 CD2
total 912 improper torsions applied
Building H-Bond parameters.
Incorporating Non-Bonded adjustments.

Warning: Parameter file was not saved.
> savepdb complex NIT101-SUB.pdb
Writing pdb file: NIT101-SUB.pdb

Warning:  Converting N-terminal residue name to PDB format: NMET -> MET

Warning:  Converting C-terminal residue name to PDB format: CPRO -> PRO
> quit
        Quit

Exiting LEaP: Errors = 4; Warnings = 6; Notes = 11.

请求大佬解答,是不是要去小分子力场参数文件里面写入报错的内容啊?但是我不知道如何写,郁闷 返回小木虫查看更多

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  • hdx1991

    你把你的leap文件让我们看下,一般是先加载蛋白力场,在加载小分子力场,小分子和蛋白的pdb文件里面要用TER隔开

  • shuigezhi

    引用回帖:
    2楼: Originally posted by hdx1991 at 2020-12-09 12:12:53
    你把你的leap文件让我们看下,一般是先加载蛋白力场,在加载小分子力场,小分子和蛋白的pdb文件里面要用TER隔开

    这是我的leap文件,根据教程来弄得,
    tleap -f oldff/leaprc.ff99SB
    source leaprc.gaff
    loadamberparams SUB_h.frcmod
    loadoff SUB.lib
    complex = loadpdb COM.pdb
    saveamberparm complex NIT101-SUB.prmtop NIT101-SUB.inpcrd
    savepdb complex NIT101-SUB.pdb
    quit

    下面是我的复合物受体和配体之间,已经用了TER隔开了
    ATOM   2244  CG  PRO A 292     -20.750 -30.825  -3.443  1.00  0.00           C  
    ATOM   2245  CD  PRO A 292     -22.161 -31.366  -3.701  1.00  0.00           C  
    ATOM   2246  OXT PRO A 292     -22.137 -28.351  -0.858  1.00  0.00           O  
    TER    2247      PRO A 292
    ATOM   2248  N   SUB d   0       7.403 -48.965 -13.607  1.00  0.00           N  
    ATOM   2249  N   SUB d   0       3.192 -50.043 -17.304  1.00  0.00           N  
    ATOM   2250  C   SUB d   0       7.078 -48.177 -19.244  1.00  0.00           C  
    ATOM   2251  C   SUB d   0       7.366 -49.172 -18.103  1.00  0.00           C  
    ATOM   2252  C   SUB d   0       7.407 -50.602 -18.668  1.00  0.00           C  
    ATOM   2253  C   SUB d   0       6.325 -48.995 -16.978  1.00  0.00           C  
    ATOM   2254  C   SUB d   0       6.369 -49.995 -15.804  1.00  0.00           C  
    ATOM   2255  C   SUB d   0       6.957 -49.411 -14.579  1.00  0.00           C  
    ATOM   2256  C   SUB d   0       5.020 -50.689 -15.523  1.00  0.00           C  
    ATOM   2257  C   SUB d   0       3.989 -50.335 -16.515  1.00  0.00           C  
    最终是NIT101-SUB.inpcrd ,这个坐标文件生成不了,是不是之前的小分子力场参数这个文件SUB_h.frcmod设置的问题??求解惑

  • hdx1991

    就是小分子力场的问题,你看看小分子的名字对不对,就是frcmod里面的名字

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