Re: [gmx-users] Virtual Sites in protein-ligand systems
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 Nicolaswrote: > 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 : > > > > > > > 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 > > > > jalem...@outerbanks.umaryland.edu | (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 gmx-users-requ...@gromacs.org. > > > -- > 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 gmx-users-requ...@gromacs.org. > -- 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 gmx-users-requ...@gromacs.org.
Re: [gmx-users] Virtual Sites in protein-ligand systems
On 10/30/15 6:11 AM, Joan Clark Nicolas 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? At present, the simplest way forward is to take the information you have in your ligand topology from acpype and create an .rtp entry, then allow pdb2gmx to process the whole thing and build the virtual sites on the ligand. 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. You can do this, but in addition to specifying the virtual sites (read in the PDF manual, it's all there), you will need to make the appropriate conversions in the [atoms] section and also build the coordinates for all virtual sites (e.g. the things that pdb2gmx does). -Justin Thank You! *Joan Clark i Nicolas* 2015-10-29 18:18 GMT+00:00 Justin Lemkul: 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 jalem...@outerbanks.umaryland.edu | (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 gmx-users-requ...@gromacs.org. -- == 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 jalem...@outerbanks.umaryland.edu | (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 gmx-users-requ...@gromacs.org.
Re: [gmx-users] Virtual Sites in protein-ligand systems
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: > > > 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 > > jalem...@outerbanks.umaryland.edu | (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 gmx-users-requ...@gromacs.org. > -- 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 gmx-users-requ...@gromacs.org.
Re: [gmx-users] Virtual Sites in protein-ligand systems
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 jalem...@outerbanks.umaryland.edu | (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 gmx-users-requ...@gromacs.org.
[gmx-users] Virtual Sites in protein-ligand systems
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? Thanks! *Joan Clark i Nicolas* -- 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 gmx-users-requ...@gromacs.org.