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

David van der Spoel spoel at xray.bmc.uu.se
Fri Oct 17 23:32:19 CEST 2008

Alberto Sergio Garay wrote:
> 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.
If you use the -ignh flag the you need to recreate hydrogens using the 
hydrogen database, If not, then all names in the coordinate file need to 
match exactly the rtp file. pdb2gmx also renames atoms according to the 
table in xlateat.dat. You may want to generate a file in your working 
directory called xlateat.dat which contains just a single zero on the 
first line. In this way no atom renaming is done.

David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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