[gmx-users] Problem building a new polymer using pdb2gmx ....

Alberto Sergio Garay sgaray at fbcb.unl.edu.ar
Fri Oct 17 21:05:47 CEST 2008


Dear David (van der Spoel)

Thank you for help again!

I'm sending a part of my gro input file, which includes the first 2
residues. The VBT 2 is the one which pdb2gmx complains about:

pdb2gmx -f polymer.gro -ter -ignh -p top

Processing chain 1 (239 atoms, 14 residues)
Fatal error:
Atom O in residue VBT 2 not found in rtp entry with 24 atoms
while sorting atoms

Generated by trjconv : 14 TEQ-VBT 1:1 t= 0000.00000
   309
     1TQL    CTL    1   3.058   5.402   1.733
     1TQL    CC2    2   3.144   5.276   1.717
     1TQL    CR1    3   3.225   5.235   1.822
     1TQL    CR2    4   3.184   5.124   1.894
     1TQL    HR2    5   3.092   5.069   1.874
     1TQL    CR3    6   3.257   5.086   2.006
     1TQL    HR3    7   3.237   4.993   2.060
     1TQL    CR4    8   3.373   5.150   2.048
     1TQL    CR5    9   3.414   5.263   1.977
     1TQL    HR5   10   3.510   5.311   1.994
     1TQL    CR6   11   3.337   5.303   1.869
     1TQL    HR6   12   3.370   5.401   1.832
     1TQL    CN4   13   3.439   5.090   2.154
     1TQL      N   14   3.558   5.089   2.242
     1TQL    CN1   15   3.575   5.230   2.281
     1TQL    CN2   16   3.664   5.062   2.144
     1TQL    CN3   17   3.522   4.977   2.330
     1TQL    CE1   18   3.523   5.373   2.263
     1TQL    CE2   19   3.817   5.054   2.153
     1TQL    CE3   20   3.588   4.905   2.448
     2VBT    CC1   21   3.221   5.305   1.589
     2VBT    CC2   22   3.143   5.334   1.460
     2VBT    CR1   23   3.115   5.221   1.384
     2VBT    CR2   24   3.196   5.155   1.293
     2VBT    HR2   25   3.305   5.159   1.298
     2VBT    CR3   26   3.132   5.074   1.200
     2VBT    HR3   27   3.198   5.003   1.151
     2VBT    CR4   28   2.995   5.068   1.175
     2VBT    CT1   29   2.948   5.023   1.052
     2VBT    NT1   30   3.028   5.038   0.928
     2VBT    CR5   31   2.919   5.144   1.263
     2VBT    HR5   32   2.810   5.142   1.268
     2VBT    CR6   33   2.977   5.208   1.372
     2VBT    HR6   34   2.916   5.232   1.459
     2VBT    CT2   35   3.070   4.916   0.874
     2VBT    HT1   36   3.009   4.827   0.860
     2VBT    CT3   37   3.190   4.911   0.804
     2VBT    CT4   38   3.245   4.779   0.750
     2VBT    CT5   39   3.264   5.027   0.784
     2VBT    OT1   40   3.364   5.030   0.712
     ........................................

Below it is a part of the rtp file which includes the VBT building block:

[ VBT ]
  [ atoms ]
; name   type   charge   chargegroup
   CC1   CH2     0.00000     1
   CC2   CH1     0.12000     2
   CR1     C    -0.12000     3
   CR2     C    -0.14000     4
   HR2    HC     0.14000     4
   CR3     C    -0.08000     5
   HR3    HC     0.08000     5
   CR4     C    -0.05000     6
   CT1   CH2     0.37000     6
   NT1    NR    -0.32000     6
   CR5     C    -0.13000     7
   HR5    HC     0.13000     7
   CR6     C    -0.17000     8
   HR6    HC     0.17000     8
   CT2     C    -0.21000     9
   HT1    HC     0.21000     9
   CT3     C    -0.09000    10
   CT4   CH3     0.09000    10
   CT5     C     0.58000    11
   OT1     O    -0.58000    11
   NT2    NR    -0.22000    12
   HT2     H     0.22000    12
   CT6     C     0.54000    13
   OT2     O    -0.54000    13
;
  [ bonds ]
; atom1 atom2 b0 kb
   CC2  +CC1    gb_27
   CC1   CC2    gb_27
   CC2   CR1    gb_15
   CR1   CR2    gb_16
   CR2   CR3    gb_16
   CR3   CR4    gb_16
   CR4   CR5    gb_16
   CR5   CR6    gb_16
   CR6   CR1    gb_16
   CR2   HR2    gb_3
   CR3   HR3    gb_3
   CR5   HR5    gb_3
   CR6   HR6    gb_3
   CR4   CT1    gb_15
   CT1   NT1    gb_23
   NT1   CT2    gb_17
   CT2   HT1    gb_3
   CT2   CT3    gb_16
   CT3   CT4    gb_27
   CT3   CT5    gb_16
   CT5   OT1    gb_5
   CT5   NT2    gb_17
   NT2   HT2    gb_2
   NT2   CT6    gb_17
   CT6   OT2    gb_5
   CT6   NT1    gb_17

  [ angles ]
;  ai    aj    ak   gromos type
  -CC2   CC1   CC2    ga_15
   CC1   CC2  +CC1    ga_15
   CR1   CC2  +CC1    ga_15
   CC1   CC2   CR1    ga_15
   CC2   CR1   CR2    ga_25
   CC2   CR1   CR6    ga_25
   CR1   CR2   CR3    ga_27
   CR2   CR3   CR4    ga_27
   CR3   CR4   CR5    ga_27
   CR4   CR5   CR6    ga_27
   CR5   CR6   CR1    ga_27
   CR6   CR1   CR2    ga_27
   CR1   CR2   HR2    ga_25
   HR2   CR2   CR3    ga_25
   CR2   CR3   HR3    ga_25
   HR3   CR3   CR4    ga_25
   CR4   CR5   HR5    ga_25
   HR5   CR5   CR6    ga_25
   CR5   CR6   HR6    ga_25
   HR6   CR6   CR1    ga_25
   CR3   CR4   CT1    ga_25
   CR5   CR4   CT1    ga_25
   CR4   CT1   NT1    ga_8
   CT1   NT1   CT2    ga_27
   CT1   NT1   CT6    ga_27
   NT1   CT2   HT1    ga_25
   NT1   CT2   CT3    ga_27
   NT1   CT6   OT2    ga_27
   NT1   CT6   NT2    ga_27
   HT1   CT2   CT3    ga_25
   CT2   CT3   CT4    ga_27
   CT2   CT3   CT5    ga_27
   CT4   CT3   CT5    ga_27
   CT3   CT5   OT1    ga_27
   CT3   CT5   NT2    ga_27
   OT1   CT5   NT2    ga_27
   CT5   NT2   HT2    ga_25
   CT6   NT2   HT2    ga_25
   CT5   NT2   CT6    ga_27
   NT2   CT6   OT2    ga_27
   CT6   NT1   CT2    ga_27
  -CCE   CC2  +CC1    ga_15
  -CCE   CC2   CR1    ga_15
;
  [ impropers ]
;  ai    aj    ak    al   gromos type
   CC2   CC1   CR1  +CC1    gi_2
; tymine ring:
; sustituyents
   NT1   CT6   CT2   CT1    gi_1
   CT6   NT1   NT2   OT2    gi_1
   CT2   NT1   CT3   HT1    gi_1
   CT3   CT2   CT5   CT4    gi_1
   CT5   CT3   NT2   OT1    gi_1
   NT2   CT5   CT6   HT2    gi_1
; ring
   NT1   CT2   CT3   CT5    gi_1
   CT2   CT3   CT5   NT2    gi_1
   CT3   CT5   NT2   CT6    gi_1
   CT5   NT2   CT6   NT1    gi_1
   NT2   CT6   NT1   CT2    gi_1
   CT6   NT1   CT2   CT3    gi_1
;
; bencene ring:
; sustituyents
   CR1   CR6   CR3   CC2    gi_1
   CR4   CR3   CR5   CT1    gi_1
   CR2   CR1   CR3   HR2    gi_1
   CR3   CR2   CR4   HR3    gi_1
   CR5   CR4   CR6   HR5    gi_1
   CR6   CR5   CR1   HR6    gi_1
; ring
   CR1   CR2   CR3   CR4    gi_1
   CR2   CR3   CR4   CR5    gi_1
   CR3   CR4   CR5   CR6    gi_1
   CR4   CR5   CR6   CR1    gi_1
   CR5   CR6   CR1   CR2    gi_1
   CR6   CR1   CR2   CR3    gi_1
;
;
  [ dihedrals ]
;  ai    aj    ak    al   gromos type
  -CC1   -CC2    CC1    CC2  gd_34
  -CC2    CC1    CC2   +CC1  gd_34
  -CC2    CC1    CC2    CR1  gd_34
   CR3    CR4    CT1    NT1  gd_10
   CR4    CT1    NT1    CT2  gd_40
   CC1    CC2    CR1    CR2  gd_40

  [ exclusions ]
;  ai    aj
CC2 HR2
CC2 CR3
CC2 HR6
CC2 CR5
CR1 HR3
CR1 HR5
CR1 CR4
CR2 HR6
CR2 CT1
HR2 HR3
HR2 CR4
HR2 CR6
CR6 CT1
CR6 CR3
CR3 HR5
CR3 NT1 ; CHECK
HR3 CR5
HR3 CT1
CR4 CT2
CR4 CT6
CT1 HT1
CT1 CT3
CT1 NT2
CT1 OT2
NT1 CT4
NT1 CT5
NT1 HT2
CT2 OT1
CT2 NT2
CT2 OT2
HT1 CT4
HT1 CT6
HT1 CT5
CT6 CT3
CT6 OT1
CT4 OT1
CT4 NT2

I tested the integrity of the rtp file using the pdb2gmx in a pdb protein
file, and it did it right.

Below it is a part of the aminoacid.dat file where I include the names  
of the residues
building block.

60
ABU
ACE
AIB
ALA
ARG
ARGN
...
...
VBT
VBL
VBR
TEQ
TQL
TQR

Finally a replace the original rtp and aminoacid files for the ones  
that I've posted.

Thank you and I'll be waiting anxiously for any clue for my problem.


-- 
Dr. Sergio Garay
Facultad de Bioquimica y Cs. Biológicas
Universidad Nacional del Litoral
Santa Fe - Argentina
C.C. 242 - Ciudad Universitaria - C.P. S3000ZAA
Argentina
Ph. +54 (342) 4575-213
Fax. +54 (342) 4575-221








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