[gmx-users] fatal error [using pdb2gmx]

[Erik Lindahl]

Hi Sven,

The problem with the glycine in the latter place is that the atom  
names/enumeration are wrong.

Gromacs relies on the standard PDB names, and then optionally adds  
the termini itself.

You can find the correct/expected atom names for each force field in  
the ffNAME.rtp file, e.g. ffoplsaa.rtp (in the share/top dir).

If there are problems with the termini you can just remove the extra  
atoms and let Gromacs recreate them for you. I've attached a proper  
GLY.pdb file with hydrogens. If you are using a united-atom force  
field (e.g. Gromos96) you need to use the -ignh option to pdb2gmx,  
though.

Cheers,

Erik
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Erik Lindahl  <lindahl at sbc.su.se>
Assistant Professor, Stockholm Bioinformatics Center
Stockholm University, SE 106 91 Stockholm
Phone: +46 8 5537 8564     Fax: +46 8 5537 8214