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

Alberto Sergio Garay sgaray at fbcb.unl.edu.ar
Fri Oct 17 22:23:28 CEST 2008

Dear David

I renamed the atom OT1 to OX1 in the gro and rtp files but pdb2gmx  
still gives me the same error:

Processing chain 1 (239 atoms, 14 residues)
There are 7 donors and 13 acceptors
There are 0 hydrogen bonds

Program pdb2gmx, VERSION 3.3.3
Source code file: pdb2gmx.c, line: 421

Fatal error:
Atom O in residue VBT 2 not found in rtp entry with 24 atoms
while sorting atoms.

It is strange that it found 14 residues (which it  is correct) but  
only 239 atoms (the system has 309 atoms) so it seems that pdb2gmx  
would have taken out all the H atoms of the system.
What are the steps that pdb2gmx follows when it works on a molecule?

I will be working on it. Thank you in advance for helping me.

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

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