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

Adriano Santana Sanchez adriano.santanasanchez at kaust.edu.sa
Fri Nov 3 09:49:13 CET 2017

 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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