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

[Justin Lemkul]

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

-- 
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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
http://www.thelemkullab.com

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