No, ACPYPE won’t give VS. But if I learn more about, I can try to implement. No guarantee though.
On 30 October 2015 at 10:11, Joan Clark Nicolas <[email protected]> wrote: > I am trying to run MD calculations using a 5 fs timestep, so I need tu use > Virtual Sites. The problem is that I generate ligand topology with acpype > and then I add it to the protein topology, so the VS of the ligand are not > generated. Maybe there is a way to generate VS for the ligand with acpype? > > And, about the [ virtual_sites* ] directive, can you tell me where can I > read about this? maybe this is the thing I am looking for. > > Thank You! > > > > *Joan Clark i Nicolas* > > 2015-10-29 18:18 GMT+00:00 Justin Lemkul <[email protected]>: > > > > > > > On 10/28/15 9:57 AM, Joan Clark Nicolas wrote: > > > >> Dear gmx users, > >> I am trying to run MD calculations on a protein-ligand system using > >> Virtual > >> Sites, but as I generate my protein and ligand topologies separately > (with > >> pdb2gmx and acpype, respectively), the VS for the ligand are not > >> generated. > >> > >> Does anyone know a way to generate the VS for the ligand without adding > it > >> to the force field? > >> > >> > > One can define any [ virtual_sites* ] directive manually in the topology. > > pdb2gmx can build some types of virtual sites, but you'd have to tell us > > specifically what it is you're trying to do if you want anything really > > useful. Soon I will upload a patch that will make virtual site > > construction easier, and intrinsic to pdb2gmx. I just need to find the > > time to work out the kinks... > > > > -Justin > > > > -- > > ================================================== > > > > Justin A. Lemkul, Ph.D. > > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > > > Department of Pharmaceutical Sciences > > School of Pharmacy > > Health Sciences Facility II, Room 629 > > University of Maryland, Baltimore > > 20 Penn St. > > Baltimore, MD 21201 > > > > [email protected] | (410) 706-7441 > > http://mackerell.umaryland.edu/~jalemkul > > > > ================================================== > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to [email protected]. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to [email protected]. > -- Alan Wilter SOUSA da SILVA, DSc Senior 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 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
