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

David van der Spoel spoel at xray.bmc.uu.se
Fri Oct 17 18:33:10 CEST 2008

Alberto Sergio Garay wrote:
> 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

This still looks like it is doing something to your termini, or you 
could have an error in the rtp file. Can you try to make a minimal 
system and post it to the list?

> 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.
> Sergio

David van der Spoel, PhD, Professor of Biology
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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