[gmx-users] Error while using the CHARMM forcefield for NAD ligand in Gromacs-2

BIJENDRA KHADKA khadkab at mcmaster.ca
Fri Sep 21 15:51:34 CEST 2018

Sorry, Please disregard this email.

On Fri, Sep 21, 2018 at 9:49 AM, BIJENDRA KHADKA <khadkab at mcmaster.ca>

> 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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