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

Justin Lemkul jalemkul at vt.edu
Thu Sep 20 23:03:12 CEST 2018

On 9/20/18 5:01 PM, BIJENDRA KHADKA wrote:
>   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).

You can't; a CHARMM .rtf is the equivalent of a GROMACS .rtp, not .itp. 
Besides, CHARMM-GUI provides you with all the files you need to run in 
GROMACS. Don't try to re-execute pdb2gmx. Just use the files it gives you.



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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