Re: [gmx-users] Charmm to Gromacs itps
@Justin, thank you Justin. I will give it a try then. @Miro, sure, I will look into it, thank you. - Yogesh On Fri, 31 Jan 2020 20:24:36 +0530 Miro Astore wrote Would topotools in vmd not work in this context? I haven't used it but readabout it recently and it would seem this is the use case. Of course youalso need parameters. Wondering.Best, MiroLe sam. 1 févr. 2020 à 00:55, Justin Lemkul a écrit :>>> On 1/31/20 8:25 AM, atb files wrote:> >> >> >> > The files are given on the following server:> https://terpconnect.umd.edu/~jbklauda/memb.htmlThey have simulated> systems using NAMD.>> If the individual topologies are not available anywhere, just a PSF,> then you will have to write your own converter program to transform the> PSF into GROMACS .top format. PSF is very verbose so this should be> straightforward.>> -Justin>> --> ==>> Justin A. Lemkul, Ph.D.> Assistant Professor> Office: 301 Fralin Hall> Lab: 303 Engel Hall>> Virginia Tech Department of Biochemistry> 340 West Campus Dr.> Blacksburg, VA 24061>> jalem...@vt.edu | (540) 231-3129> http://www.thelemkullab.com>> ==>> --> 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 visithttps://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] Charmm to Gromacs itps
Would topotools in vmd not work in this context? I haven't used it but read about it recently and it would seem this is the use case. Of course you also need parameters. Wondering. Best, Miro Le sam. 1 févr. 2020 à 00:55, Justin Lemkul a écrit : > > > On 1/31/20 8:25 AM, atb files wrote: > > > > > > > > The files are given on the following server: > https://terpconnect.umd.edu/~jbklauda/memb.htmlThey have simulated > systems using NAMD. > > If the individual topologies are not available anywhere, just a PSF, > then you will have to write your own converter program to transform the > PSF into GROMACS .top format. PSF is very verbose so this should be > straightforward. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > == > > -- > 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] Charmm to Gromacs itps
On 1/31/20 8:25 AM, atb files wrote: The files are given on the following server:https://terpconnect.umd.edu/~jbklauda/memb.htmlThey have simulated systems using NAMD. If the individual topologies are not available anywhere, just a PSF, then you will have to write your own converter program to transform the PSF into GROMACS .top format. PSF is very verbose so this should be straightforward. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- 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] Charmm to Gromacs itps
The files are given on the following server:https://terpconnect.umd.edu/~jbklauda/memb.htmlThey have simulated systems using NAMD. -Yogesh On Thu, 30 Jan 2020 19:45:16 +0530 Justin Lemkul wrote On 1/28/20 3:35 AM, atb files wrote: > > > > @Justin: the lipid is not yet added to the charmm directory. Any script? How did you produce the original PSF? -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- 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] Charmm to Gromacs itps
On 1/28/20 3:35 AM, atb files wrote: @Justin: the lipid is not yet added to the charmm directory. Any script? How did you produce the original PSF? -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- 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] Charmm to Gromacs itps
@Justin: the lipid is not yet added to the charmm directory. Any script?@Michele: pdb2gmx only works for proteins.-YogeshSent using Zoho Mail On Mon, 27 Jan 2020 19:34:34 +0530 Justin Lemkul wrote On 1/27/20 4:51 AM, atb files wrote:> >> > Hello users,I have .pdb, .psf and .crd file for one system. How to use them (convert to itp) in Gromacs? Thanks. YogesgSent using Zoho Mail> >Prepare the system with CHARMM-GUI and it will give you all the necessary inputs for running in GROMACS.-Justin-- ==Justin A. Lemkul, Ph.D.Assistant ProfessorOffice: 301 Fralin HallLab: 303 Engel HallVirginia Tech Department of Biochemistry340 West Campus Dr.Blacksburg, VA 24061jalem...@vt.edu | (540) 231-3129http://www.thelemkullab.com==-- 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 visithttps://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] Charmm to Gromacs itps
On 1/27/20 4:51 AM, atb files wrote: Hello users,I have .pdb, .psf and .crd file for one system. How to use them (convert to itp) in Gromacs? Thanks. YogesgSent using Zoho Mail Prepare the system with CHARMM-GUI and it will give you all the necessary inputs for running in GROMACS. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- 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] Charmm to Gromacs itps
Hi, have you tried gmx pdb2gmx -f ? Michele From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of atb files Sent: 27 January 2020 10:51 To: gromacs.org_gmx-users Subject: [gmx-users] Charmm to Gromacs itps Hello users,I have .pdb, .psf and .crd file for one system. How to use them (convert to itp) in Gromacs? Thanks. YogesgSent using Zoho Mail -- 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] Charmm to Gromacs itps
Hello users,I have .pdb, .psf and .crd file for one system. How to use them (convert to itp) in Gromacs? Thanks. YogesgSent using Zoho Mail -- 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.
