[gmx-users] gmx pdb2gmx

Justin Lemkul jalemkul at vt.edu
Thu Sep 20 16:37:09 CEST 2018

On 9/20/18 7:21 AM, antonia vyrkou wrote:
> Hello!
> I want to create a topology file for a LDHA-NADH-PYRUVATE system.
> I have created the pdb file, copied the .rtp in the relevant directory and
> added a       [ bond ] and [ impropers ] section for pyruvate.
> When I run gmx pdb2gmx I get two warnings and a fatal error.
> The warnings are:
> Warning: Starting residue NAD801 in chain not identified as Protein/RNA/DNA.
> Warning: Starting residue PYR802 in chain not identified as Protein/RNA/DNA.
> NADH and Pyruvate are not enzymes, how should I specify them in the
> residuetypes.dat file?

These are merely advisory; they will not cause a problem as long as all 
.rtp entries are properly defined.

> The fatal error is:
> Residue 'PYR' not found in residue topology database
> Doesn't gmx pdb2gmx use as input the local rtp file where PYR is specified?

The .rtp file must be in the force field subdirectory that you're using.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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