[gmx-users] Ligand breaking in to two

Alan alanwilter at gmail.com
Mon Oct 21 11:33:27 CEST 2013

Have you tested your ligand alone in MD simulation and how vmd would show


On 21 October 2013 08:31, MUSYOKA THOMMAS <mutemibiochemistry at gmail.com>wrote:

> Dear Users,
> I am doing protein-ligand MD simulations. I first prepare the ligand by
> adding Hydrogen atoms and setting the charges using UCSF chimera. I
> thereafter use acpype to get the ligand's gro,itp and top files. Finally, i
> process the protein.PDB file and perform MD simulations. However, when I
> combine the ligand and protein gro files and convert the resulting complex
> to a PDB file so as to visualise with VMD, the ligand always appears to be
> broken in two parts.
> Any advice on how to overcome this?
> Thanks
> --
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Alan Wilter SOUSA da SILVA, DSc
Bioinformatician, UniProt
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Cambridge CB10 1SD
United Kingdom
Tel: +44 (0)1223 494588

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