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

Vytautas Rakeviius vytautas1987 at yahoo.com
Fri Nov 3 10:06:28 CET 2017

It seems that ctab.pdb contains residue 'XXX'. Verify that with pdb viewer such as pymol etc.
 Residue 'XXX' is not standard amino acid with 3 letter code so in lead to such error.Maybe you can delete it with same pdb viewer, or fix that naming error somehow. Its up to you to decide.

    On Friday, November 3, 2017, 10:49:27 AM GMT+2, Adriano Santana Sanchez <adriano.santanasanchez at kaust.edu.sa> 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?



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