[gmx-users] pdb (CTAB) into .GRO

Justin Lemkul jalemkul at vt.edu
Fri Nov 3 13:19:44 CET 2017

On 11/3/17 4:49 AM, Adriano Santana Sanchez wrote:
>   Dear all,
>   I am a beginner with gromacs and I have already done some online tutorials.
>   I am now trying to create from a PDB coordinate file (a CTAB molecule) the
>   corresponding .GRO and .TOP files to run MD simulations.
>   gmx pdb2gmx -f ctab.pdb -o ctab_processed.gro -water spce
>   then choose FF gromos96 53a6 but get error message:
>   Residue 'XXX' not found in topology database
> I am sure this FF has been used for this molecule before and I cannot
> find this CTAB on the residue database. What can I do?

pdb2gmx cannot process something it doesn't know about, so if a residue 
is not in the .rtp file, you can't use that force field unless you (1) 
find parameters in the literature and add them to the .rtp and force 
field files or (2) parametrize it yourself and subsequently add it.



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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