Re: [gmx-users] Using pdb2gmx with martini (coarse-grained) model to assign termini charges
Hi Sourav, For Martini there's the conversion script martinize, which has an option -nt to suppress putting charges on termini. This is not really a Gromacs question, and it's better to post Martini related questions on the forum at http://cgmartini.nl Cheers, Tsjerk On May 24, 2016 23:35, "Justin Lemkul"wrote: > > > On 5/24/16 5:33 PM, Sourav Ray wrote: > >> Hello >> >> Thanks for your answer, I presume pdb2gmx needs some force-field >> definitions to work, anyway, can I assign charges selectively to certain >> atom number? Let me know if it is feasible, I searched the forums but >> couldn't find anything specific. >> >> > Try some MARTINI tutorials; IIRC topology generation is not typically done > via pdb2gmx. > > -Justin > > Regards >> Sourav >> >> On Wed, May 25, 2016 at 2:48 AM, Mark Abraham >> wrote: >> >> Hi, >>> >>> If you've already arranged your own termini, then you can choose "None" >>> from the options pdb2gmx presents. >>> >>> Mark >>> >>> On Tue, May 24, 2016 at 11:15 PM Sourav Ray >>> wrote: >>> >>> Hello I am trying to put selective charges on the termini, I am getting stuck >>> at >>> the initial stage where I am supposed to mention the force-field needed. >>> As >>> martini termini differ from conventional ones, I am unable to bypass NH3+ or COO- termini options at the start and end respectively as there is no appropriate force-field option present there. Please let me know if >>> anyone >>> has a workaround. Regards Sourav -- 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. >>> >>> > -- > == > > 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] Using pdb2gmx with martini (coarse-grained) model to assign termini charges
On 5/24/16 5:33 PM, Sourav Ray wrote: Hello Thanks for your answer, I presume pdb2gmx needs some force-field definitions to work, anyway, can I assign charges selectively to certain atom number? Let me know if it is feasible, I searched the forums but couldn't find anything specific. Try some MARTINI tutorials; IIRC topology generation is not typically done via pdb2gmx. -Justin Regards Sourav On Wed, May 25, 2016 at 2:48 AM, Mark Abrahamwrote: Hi, If you've already arranged your own termini, then you can choose "None" from the options pdb2gmx presents. Mark On Tue, May 24, 2016 at 11:15 PM Sourav Ray wrote: Hello I am trying to put selective charges on the termini, I am getting stuck at the initial stage where I am supposed to mention the force-field needed. As martini termini differ from conventional ones, I am unable to bypass NH3+ or COO- termini options at the start and end respectively as there is no appropriate force-field option present there. Please let me know if anyone has a workaround. Regards Sourav -- 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. -- == 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] Using pdb2gmx with martini (coarse-grained) model to assign termini charges
Hello Thanks for your answer, I presume pdb2gmx needs some force-field definitions to work, anyway, can I assign charges selectively to certain atom number? Let me know if it is feasible, I searched the forums but couldn't find anything specific. Regards Sourav On Wed, May 25, 2016 at 2:48 AM, Mark Abrahamwrote: > Hi, > > If you've already arranged your own termini, then you can choose "None" > from the options pdb2gmx presents. > > Mark > > On Tue, May 24, 2016 at 11:15 PM Sourav Ray wrote: > > > Hello > > > > I am trying to put selective charges on the termini, I am getting stuck > at > > the initial stage where I am supposed to mention the force-field needed. > As > > martini termini differ from conventional ones, I am unable to bypass NH3+ > > or COO- termini options at the start and end respectively as there is no > > appropriate force-field option present there. Please let me know if > anyone > > has a workaround. > > > > Regards > > Sourav > > -- > > 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. > -- 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] Using pdb2gmx with martini (coarse-grained) model to assign termini charges
Hello I am trying to put selective charges on the termini, I am getting stuck at the initial stage where I am supposed to mention the force-field needed. As martini termini differ from conventional ones, I am unable to bypass NH3+ or COO- termini options at the start and end respectively as there is no appropriate force-field option present there. Please let me know if anyone has a workaround. Regards Sourav -- 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] Using pdb2gmx with martini (coarse-grained) model to assign termini charges
Hi, If you've already arranged your own termini, then you can choose "None" from the options pdb2gmx presents. Mark On Tue, May 24, 2016 at 11:15 PM Sourav Raywrote: > Hello > > I am trying to put selective charges on the termini, I am getting stuck at > the initial stage where I am supposed to mention the force-field needed. As > martini termini differ from conventional ones, I am unable to bypass NH3+ > or COO- termini options at the start and end respectively as there is no > appropriate force-field option present there. Please let me know if anyone > has a workaround. > > Regards > Sourav > -- > 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.
[gmx-users] Using pdb2gmx with martini (coarse-grained) model to assign termini charges
Hello I am trying to put selective charges on the termini, I am getting stuck at the initial stage where I am supposed to mention the force-field needed. As martini termini differ from conventional ones, I am unable to bypass NH3+ or COO- termini options at the start and end respectively as there is no appropriate force-field option present there. Please let me know if anyone has a workaround. Regards Sourav -- 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.