[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
it?

Alan


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
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



-- 
Alan Wilter SOUSA da SILVA, DSc
Bioinformatician, UniProt
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom
Tel: +44 (0)1223 494588



More information about the gromacs.org_gmx-users mailing list