[gmx-users] Message-ID: <d3e21a78-9b0c-88fa-a6d7-c60c56a0e488 at vt.edu>

BIJENDRA KHADKA khadkab at mcmaster.ca
Thu Sep 20 23:01:16 CEST 2018

 Dear Justin,
Thank you for your suggestion. I tried to process the ligand(NAD) with
pdb2gmx, however, received the following error despite correct atom name in
PDB file (file attached) relative to NAD information in merged.itp.
In case of CHARMM-GUI, it provides a NAD.rtf and .prm as output, while
Gromacs required an .itp as input. (How to convert .rtf file to .itp file).

Command: /gmx pdb2gmx -f NAD.pdb -i NAD.itp

Fatal error:
Atom HN in residue NAD 1 was not found in rtp entry NAD with 70 atoms
while sorting atoms.

KInd Regards,


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