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

[Alberto Sergio Garay]

Dear users

I'm trying to build a polymer with a new building block. I have  
included the new
topology block inside the force field rtp file, which I've choosen for  
my simulation (ffG53a6.rtp).
I've also prepared a gro input file, where the atoms of each residue  
follows the same order as in the rtp file
I also added the new residues names in aminoacids.dat

The problem is: when I run pdb2gmx to obtain the topology of my system  
it gives me the following error:

Fatal error:
Atom H1 in residue VBT 2 not found in rtp entry with 24 atoms
              while sorting atoms. Maybe different protonation state.
              Remove this hydrogen or choose a different protonation state.
              Option -ignh will ignore all hydrogens in the input.

But there's no H1 atom in my residues. Is pdb2gmx including some extra  
atoms to complete my molecule?
Could anyone give any clue about my problem?

Tank you in advance.

Sergio

below there's a part of my rtp file
...
[ 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

part of my *.gro file

     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
     2VBT    NT2   41   3.224   5.150   0.839
     2VBT    HT2   42   3.293   5.223   0.844
     2VBT    CT6   43   3.100   5.156   0.903
     2VBT    OT2   44   3.076   5.266   0.952

-- 
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