[gmx-users] gmx pdb2gmx
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
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?
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