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

Alberto Sergio Garay sgaray at fbcb.unl.edu.ar
Fri Oct 17 15:22:50 CEST 2008

Dear David (van der Spoel)

Thank you for your time.

Firstly: I don't need to add any H atom to my polymer. All atoms that I
need are in the rtp topology file. So I did not change the hdb file.

Using this command (as you suggested in the last message):

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

Below  I extracted the main differences with the previous pdb2gmx error:

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

Evidently, pdb2gmx is doing something funny with my polymer, because  
it found 239 atoms in my gro file, when it really contains 309.  
Without the option -ignh (as I did it before) it found the correct  
number of atoms (309).
Finally it also found the atom O in my gro files, which (again) it  
doesn't really exist.

What is pdb2gmx doing? I don't understand what I am doing wrong.
Any suggestion will be appreciated.


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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