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jianana

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注册: 2012-02-28
性别: MM
专业: 理论和计算化学

[求助] gromacs 添加新的力场pdb2gmx报错

我现在做一个小分子，gromacs中没有这个分子的残基，我的pdb文件如下：
HETATM 3 CA LIG    1    4.784 1.069  -0.170  1.00  0.00          C
HETATM 4 CA LIG    1    3.605 1.699  -0.680  1.00  0.00          C
HETATM 5 HA LIG    1    3.443 2.015  -1.706  1.00  0.00          H
HETATM 6 CA LIG    1    2.659 1.795 0.388  1.00  0.00          C
HETATM 7 HA LIG    1    1.649 2.180 0.313  1.00  0.00          H
HETATM 8 CA LIG    1    4.565 0.777 1.213  1.00  0.00          C
HETATM 9 HA LIG    1    5.261 0.271 1.876  1.00  0.00          H
HETATM 10 CA LIG    1    3.252 1.226 1.558  1.00  0.00          C
HETATM 11 HA LIG    1    2.776 1.123 2.528  1.00  0.00          H
HETATM 12 HA LIG    1    5.674 0.822  -0.740  1.00  0.00          H
HETATM 13 CA LIG    2    3.580  -1.941  -0.985  1.00  0.00          C
HETATM 14 CA LIG    2    2.434  -1.302  -1.537  1.00  0.00          C
HETATM 15 HA LIG    2    2.323  -0.937  -2.552  1.00  0.00          H
HETATM 16 CA LIG    2    1.442  -1.191  -0.503  1.00  0.00          C
HETATM 17 CA LIG    2    3.311  -2.230 0.390  1.00  0.00          C
HETATM 18 HA LIG    2    3.999  -2.689 1.093  1.00  0.00          H
HETATM 19 CA LIG    2    1.998  -1.768 0.694  1.00  0.00          C
HETATM 20 HA LIG    2    1.515  -1.836 1.665  1.00  0.00          H
HETATM 21 HA LIG    2    4.511  -2.140  -1.507  1.00  0.00          H
HETATM 22 FE LIG    2    3.152  -0.185 0.045  1.00  0.00       Fe
HETATM 23 HA LIG    2    0.425  -1.247  -0.870  1.00  0.00          H
CONECT 3 12 4 8
CONECT 4 5 3 6
CONECT 5 4
CONECT 6 4 7 10
CONECT 7 6
CONECT 8 3 10 9
CONECT 9 8
CONECT 10 6 8 11
CONECT 11 10
CONECT 12 3
CONECT 13 14 21 17
CONECT 14 15 13 16
CONECT 14 14
CONECT 15 14 23 22 19
CONECT 16
CONECT 17 13 19 18
CONECT 18 17
CONECT 19 16 17 20
CONECT 20 19
CONECT 21 13
CONECT 22 16
CONECT 23 16
MASTER       0 0 0 0 0 0 0 0 21 0 21 0
END
我是在oplsaa.ff中添加的参数：
1. 在ffbonded.itp中加入 [ bondtypes ]
   CA CA    1 0.14400 rigid    ; the cp ring is a rigid pentagon
   HA CA    1 0.10800 rigid    ; the bonds to hydrogen atoms are always rigid
   Fe CA    1 0.20600    190.0 ; keep iron between cps (small value to avoid divergence)
   cp cp    1 0.33200 999900.0 ; keep cps apart (not rigid due to convergence problems)
                              [ angletypes ]
      CA    CA    CA    1 108.0    rigid    ; keep cp pentagon rigid
   CA    CA    HA    1 126.0    292.9    ; in all fecps but decamethylferrocene (cp*)
      CA    xcp xcp    1 90.0    999.9    ; keep cp rings parallel, avoid tilt
                        [ dihedraltypes ]
         CA    CA    CA    CA    3    rigid                                           ; rigid cp pentagon
         CA    HA    CA    CA    3    0.0000 0.0000 9.2000 0.0000 0.0000 0.0000 ; improper in all but cp*
2.在atomtypes.atp中添加
      opls_966 55.847 ; iron
      opls_967 12.011 ; carbon in cyclopentadienyl (cp)
      opls_970 1.008 ; cp hydrogen
      opls_973 0.001 ;Xcp dummy cp centroid
3. 在ffnonbonded.itp添加
         opls_966 Fe    26 55.847    +0.10       A 3.11       2.016
      opls_967 CA    6  12.011    -0.10       A 3.55       0.293
      opls_970 HA    1 1.008    +0.09       A 2.42       0.126
      opls_973 Xcp 0 0.001    0.00       A 0.00       0.000
4 最后，我在aminoacids.rtp中添加残基【LIG】如下

[ LIG ]
  [ atoms ]
  Xcp1 opls_973 0.00    1
  Xcp2 opls_973 0.00    1
CA1 opls_967 -0.10    2
HA1 opls_970 0.09    2
CA2 opls_967 -0.10    2
HA2 opls_970 0.09    2
CA3 opls_967 -0.10    2
HA3 opls_970 0.09    2
CA4 opls_967 -0.10    2
HA4 opls_970 0.09    2
CA5 opls_967 -0.10    2
HA5 opls_970 0.09    2
CA6 opls_967 -0.10    2
HA6 opls_970 0.09    2
CA7 opls_967 -0.10    2
HA7 opls_970 0.09    2
CA8 opls_967 -0.10    2
HA8 opls_970 0.09    2
CA9 opls_967 -0.10    2
HA9 opls_970 0.09    2
  CA10 opls_967 -0.10    2
  HA10 opls_970 0.09    2
FE opls_966 0.10    2
[ bonds ]
CA1 FE
CA2 FE
CA3 FE
CA4 FE
CA5 FE
CA6 FE
CA7 FE
CA8 FE
CA9 FE
CA10 FE
[ angles ]
;  ai aj ak funct
CA1  Xcp2  Xcp1    1
CA2  Xcp2  Xcp1    1
CA3  Xcp2  Xcp1    1
CA4  Xcp2  Xcp1    1
CA5  Xcp2  Xcp1    1
CA6  Xcp1  Xcp2    1
CA7  Xcp1  Xcp2    1
CA8  Xcp1  Xcp2    1
CA9  Xcp1  Xcp2    1
  CA10  Xcp1  Xcp2    1
CA5 CA1 HA1    1
CA2 CA1 HA1    1
CA1 CA2 HA2    1
CA3 CA2 HA2    1
CA2 CA3 HA3    1
CA4 CA3 HA3    1
CA3 CA4 HA4    1
CA5 CA4 HA4    1
CA4 CA5 HA5    1
CA1 CA5 HA5    1
  CA10 CA6 HA6    1
CA7 CA6 HA6    1
CA6 CA7 HA7    1
CA8 CA7 HA7    1
CA7 CA8 HA8    1
CA9 CA8 HA8    1
CA8 CA9 HA9    1
  CA10 CA9 HA9    1
CA9  CA10  HA10    1
CA6  CA10  HA10    1
[ dihedrals ]
;  ai aj ak al funct
CA1  Xcp2  Xcp1 CA6    3
CA2  Xcp2  Xcp1 CA6    3
CA3  Xcp2  Xcp1 CA6    3
CA4  Xcp2  Xcp1 CA6    3
CA5  Xcp2  Xcp1 CA6    3
CA1  Xcp2  Xcp1 CA7    3
CA2  Xcp2  Xcp1 CA7    3
CA3  Xcp2  Xcp1 CA7    3
CA4  Xcp2  Xcp1 CA7    3
CA5  Xcp2  Xcp1 CA7    3
CA1  Xcp2  Xcp1 CA8    3
CA2  Xcp2  Xcp1 CA8    3
CA3  Xcp2  Xcp1 CA8    3
CA4  Xcp2  Xcp1 CA8    3
CA5  Xcp2  Xcp1 CA8    3
CA1  Xcp2  Xcp1 CA9    3
CA2  Xcp2  Xcp1 CA9    3
CA3  Xcp2  Xcp1 CA9    3
CA4  Xcp2  Xcp1 CA9    3
CA5  Xcp2  Xcp1 CA9    3
CA1  Xcp2  Xcp1  CA10    3
CA2  Xcp2  Xcp1  CA10    3
CA3  Xcp2  Xcp1  CA10    3
CA4  Xcp2  Xcp1  CA10    3
CA5  Xcp2  Xcp1  CA10    3
HA1 CA1 CA2 HA2    3
HA1 CA1 CA2 CA3    3
CA5 CA1 CA2 HA2    3
HA2 CA2 CA3 HA3    3
HA2 CA2 CA3 CA4    3
CA1 CA2 CA3 HA3    3
HA3 CA3 CA4 HA4    3
HA3 CA3 CA4 CA5    3
CA2 CA3 CA4 HA4    3
HA4 CA4 CA5 HA5    3
HA4 CA4 CA5 CA1    3
CA3 CA4 CA5 HA5    3
HA5 CA5 CA1 HA1    3
HA5 CA5 CA1 CA2    3
CA4 CA5 CA1 HA1    3
HA6 CA6 CA7 HA7    3
HA6 CA6 CA7 CA8    3
  CA10 CA6 CA7 HA7    3
HA7 CA7 CA8 HA8    3
HA7 CA7 CA8 CA9    3
CA6 CA7 CA8 HA8    3
HA8 CA8 CA9 HA9    3
HA8 CA8 CA9  CA10    3
CA7 CA8 CA9 HA9    3
HA9 CA9  CA10  HA10    3
HA9 CA9  CA10 CA6    3
CA8 CA9  CA10  HA10    3
  HA10  CA10 CA6 HA6    3
  HA10  CA10 CA6 CA7    3
CA9  CA10 CA6 HA6    3
  [ impropers ]
;  ai aj ak al funct          c0
CA1 HA1 CA2 CA5    1    improper_CA_HA_CA_CA
CA1 HA1 CA5 CA3    1    improper_CA_HA_CA_CA
CA2 HA2 CA3 CA1    1    improper_CA_HA_CA_CA
CA2 HA2 CA1 CA3    1    improper_CA_HA_CA_CA
CA3 HA3 CA4 CA2    1    improper_CA_HA_CA_CA
CA3 HA3 CA2 CA4    1    improper_CA_HA_CA_CA
CA4 HA4 CA5 CA3    1    improper_CA_HA_CA_CA
CA4 HA4 CA3 CA5    1    improper_CA_HA_CA_CA
CA5 HA5 CA1 CA4    1    improper_CA_HA_CA_CA
CA5 HA5 CA4 CA1    1    improper_CA_HA_CA_CA
CA6 HA6 CA7  CA10    1    improper_CA_HA_CA_CA
CA6 HA6  CA10 CA7    1    improper_CA_HA_CA_CA
CA7 HA7 CA8 CA6    1    improper_CA_HA_CA_CA
CA7 HA7 CA6 CA8    1    improper_CA_HA_CA_CA
CA8 HA8 CA9 CA7    1    improper_CA_HA_CA_CA
CA8 HA8 CA7 CA9    1    improper_CA_HA_CA_CA
CA9 HA9  CA10 CA8    1    improper_CA_HA_CA_CA
CA9 HA9 CA8  CA10    1    improper_CA_HA_CA_CA
  CA10  HA10 CA6 CA9    1    improper_CA_HA_CA_CA
  CA10  HA10 CA9 CA6    1    improper_CA_HA_CA_CA
现在我运行pdb2gmx -f *.pdb -o *.gro -p *.top命令出错
Back Off! I just backed up ferrocene.top to ./#ferrocene.top.3#
Processing chain 1 (23 atoms, 2 residues)
There are 0 donors and 0 acceptors
There are 0 hydrogen bonds
Warning: Starting residue LIG1 in chain not identified as Protein/RNA/DNA.
Warning: Starting residue LIG2 in chain not identified as Protein/RNA/DNA.
Problem with chain definition, or missing terminal residues.
This chain does not appear to contain a recognized chain molecule.
If this is incorrect, you can edit residuetypes.dat to modify the behavior.
8 out of 8 lines of specbond.dat converted successfully

-------------------------------------------------------
Program pdb2gmx, VERSION 4.5.4
Source code file: pdb2gmx.c, line: 655

Fatal error:
Atom cp in residue LIG 1 was not found in rtp entry LIG with 23 atoms
while sorting atoms.
.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

请问大家，这是什么原因呢？写这个力场已经用了我快一个月的时间了，到现在还是不对，都快崩溃了！希望大家帮帮忙啊！在此谢过！

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