[gmx-users] problems in rtp while runing pdb2gmx

Fri Jan 25 13:16:36 CET 2008

Dear all, could anybody know how to tackle the problem? I have such pdb file

  HETATM 1 CB1 DRG 1 -5.058 1.624 -0.274 1.00 C
  HETATM 2 HB11 DRG 1 -4.785 2.632 0.071 1.00 H
  HETATM 3 HB12 DRG 1 -6.149 1.562 -0.397 1.00 H
  HETATM 4 HB13 DRG 1 -4.568 1.422 -1.238 1.00 H
  HETATM 5 CG1 DRG 1 -4.605 0.597 0.750 1.00 C
  HETATM 6 HG11 DRG 1 -3.935 1.170 1.408 1.00 H
  HETATM 7 HG12 DRG 1 -5.530 0.351 1.292 1.00 H
  HETATM 8 SA DRG 1 -3.772 -0.918 -0.015 1.00 S
  HETATM 9 SB DRG 1 -1.851 -0.088 -0.732 1.00 S
  HETATM 10 CG2 DRG 1 -0.742 -0.380 0.787 1.00 C
  HETATM 11 HG21 DRG 1 -0.977 0.268 1.645 1.00 H
  HETATM 12 HG22 DRG 1 -0.702 -1.428 1.118 1.00 H
  HETATM 13 C1 DRG 1 0.673 -0.045 0.446 1.00 C
  HETATM 14 C2 DRG 1 1.694 -1.104 0.050 1.00 C
  HETATM 15 CB2 DRG 1 1.976 -2.108 1.178 1.00 C
  HETATM 16 HB21 DRG 1 1.103 -2.166 1.844 1.00 H
  HETATM 17 HB22 DRG 1 2.854 -1.777 1.752 1.00 H
  HETATM 18 HB23 DRG 1 2.173 -3.100 0.745 1.00 H
  HETATM 19 CB3 DRG 1 1.344 -1.842 -1.250 1.00 C
  HETATM 20 HB31 DRG 1 0.469 -1.367 -1.717 1.00 H
  HETATM 21 HB32 DRG 1 1.113 -2.894 -1.024 1.00 H
  HETATM 22 HB33 DRG 1 2.199 -1.794 -1.940 1.00 H
  HETATM 23 CA DRG 1 1.203 1.171 0.459 1.00 C
  HETATM 24 HA DRG 1 0.585 2.037 0.737 1.00 H
  HETATM 25 C3 DRG 1 2.660 1.200 0.069 1.00 C
  HETATM 26 CB4 DRG 1 2.912 1.990 -1.222 1.00 C
  HETATM 27 HB41 DRG 1 2.761 3.063 -1.031 1.00 H
  HETATM 28 HB42 DRG 1 2.211 1.654 -2.000 1.00 H
  HETATM 29 HB43 DRG 1 3.945 1.819 -1.560 1.00 H
  HETATM 30 CB5 DRG 1 3.566 1.706 1.199 1.00 C
  HETATM 31 HB51 DRG 1 3.133 2.618 1.636 1.00 H
  HETATM 32 HB52 DRG 1 4.564 1.931 0.795 1.00 H
  HETATM 33 HB53 DRG 1 3.650 0.932 1.976 1.00 H
  HETATM 34 N DRG 1 2.872 -0.241 -0.157 1.00 N
  HETATM 35 O DRG 1 4.010 -0.715 -0.511 1.00 O
  CONECT 1 5 2 3 4
  CONECT 2 1
  CONECT 3 1
  CONECT 4 1
  CONECT 5 1 8 6 7
  CONECT 6 5
  CONECT 7 5
  CONECT 8 5 9
  CONECT 9 8 10
  CONECT 10 9 13 11 12
  CONECT 11 10
  CONECT 12 10
  CONECT 13 10 14 23
  CONECT 14 13 15 19 34
  CONECT 15 14 16 17 18
  CONECT 16 15
  CONECT 17 15
  CONECT 18 15
  CONECT 19 14 20 21 22
  CONECT 20 19
  CONECT 21 19
  CONECT 22 19
  CONECT 23 13 25 24
  CONECT 24 23
  CONECT 25 23 26 30 34
  CONECT 26 25 27 28 29
  CONECT 27 26
  CONECT 28 26
  CONECT 29 26
  CONECT 30 25 31 32 33
  CONECT 31 30
  CONECT 32 30
  CONECT 33 30
  CONECT 34 14 25 35
  CONECT 35 34
  END

  and I put at the end of my rtp file this residue

  [ DRG ]
  [ atoms ]
  CB1 opls_135 -0.487 1
  HB11 opls_140 0.181 1
  HB12 opls_140 0.200 1
  HB13 opls_140 0.211 1
  CG1 opls_157 -0.603 1
  HG11 opls_140 0.226 1
  HG12 opls_140 0.221 1
  SA opls_202 0.049 1
  SB opls_202 0.089 1
  CG2 opls_157 -0.720 1
  HG21 opls_140 0.236 1
  HG22 opls_140 0.251 1
  C1 opls_145 0.176 1
  C2 opls_145 0.004 1
  CB2 opls_135 -0.462 1
  HB21 opls_140 0.207 1
  HB22 opls_140 0.174 1
  HB23 opls_140 0.181 1
  CB3 opls_135 -0.456 1
  HB31 opls_140 0.192 1
  HB32 opls_140 0.189 1
  HB33 opls_140 0.199 1
  CA opls_224B -0.092 1
  HA opls_140 0.164 1
  C3 opls_145 0.029 1
  CB4 opls_135 -0.457 1
  HB41 opls_140 0.173 1
  HB42 opls_140 0.187 1
  HB43 opls_140 0.201 1
  CB5 opls_135 -0.458 1
  HB51 opls_140 0.173 1
  HB52 opls_140 0.202 1
  HB53 opls_140 0.181 1
  N opls_238 -0.229 1
  O opls_236 -0.332 1
  [ bonds ]
  CB1 HB11 
  CB1 HB12
  CB1 HB13
  CB1 CG1
  CG1 HG11
  CG1 HG12
  CG1 SA
  SA SB
  SB CG2
  CG2 HG21
  CG2 HG22
  CG2 C1
  C1 C2
  C2 CB2
  C2 CB3
  C2 N
  CB2 HB21
  CB2 HB22
  CB2 HB23
  CB3 HB31
  CB3 HB32
  CB3 HB33
  N O
  N C3
  C3 CB4
  C3 CB5
  C3 CA
  CB4 HB41
  CB4 HB42
  CB4 HB43 
  CB5 HB51
  CB5 HB52
  CB5 HB53
  C1 CA
  CA HA

  [ impropers ]
  CA C2 C1 CG2 improper_Z_CA_X_Y 
  C1 C3 CA HA improper_Z_CA_X_Y 
  C2 C3 N O improper_Z_N_X_Y 
  C1 N C2 CB2 improper_O_C_X_Y 
  CA N C3 CB4 improper_O_C_X_Y 

  I've got this error

  -------------------------------------------------------
Program pdb2gmx_d, VERSION 3.3.2
Source code file: resall.c, line: 289
  Fatal error:
in .rtp file at line:

-------------------------------------------------------

  Something is wrong with my rtp, but I have no clue what (maybe impropers or bonds). Thank you in advance

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