[gmx-users] gmx pdb2gmx

antonia vyrkou avyrkou at gmail.com
Thu Sep 20 13:21:21 CEST 2018


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?

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?

Thank you

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