Re: [gmx-users] Topolgen and topolbuild
Thanks which of the CHARMM FFs from GMX library is correct for a fluorinated molecule? Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] Midtun 6894 Vangsnes Norge Org.nr. 911 659 654 Tlf: +47 57695621 [ http://www.oekolab.com/ | Økolab ] | [ http://www.nanofact.no/ | Nanofactory ] | [ http://www.aq-lab.no/ | AQ-Lab ] | [ http://www.phap.no/ | FAP ] From: "Justin Lemkul" <jalem...@vt.edu> To: "gmx-users" <gmx-us...@gromacs.org> Sent: Wednesday, October 4, 2017 12:41:50 PM Subject: Re: [gmx-users] Topolgen and topolbuild On 10/4/17 6:09 AM, Sergio Manzetti wrote: > Hi Stephane. Thanks for that. I have tried it, however it generates a str > file, and from there how to generate the GMX ITP is unknown. > > Is there a tutorial that shows how to generate ITP from STR? Use our conversion script: http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- 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] Topolgen and topolbuild
On 10/4/17 6:09 AM, Sergio Manzetti wrote: Hi Stephane. Thanks for that. I have tried it, however it generates a str file, and from there how to generate the GMX ITP is unknown. Is there a tutorial that shows how to generate ITP from STR? Use our conversion script: http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- 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] Topolgen and topolbuild
PS: generate ITP from STR without CHARMM GUI Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] Midtun 6894 Vangsnes Norge Org.nr. 911 659 654 Tlf: +47 57695621 [ http://www.oekolab.com/ | Økolab ] | [ http://www.nanofact.no/ | Nanofactory ] | [ http://www.aq-lab.no/ | AQ-Lab ] | [ http://www.phap.no/ | FAP ] From: "ABEL Stephane" <stephane.a...@cea.fr> To: "gromacs org gmx-users" <gromacs.org_gmx-users@maillist.sys.kth.se> Sent: Wednesday, October 4, 2017 12:15:19 PM Subject: [gmx-users] Topolgen and topolbuild Hi if your molecule is a ligand, you could use ParamChem (https://cgenff.paramchem.org/) Stéphane -- Message: 1 Date: Wed, 4 Oct 2017 10:10:24 +0200 (CEST) From: Sergio Manzetti <sergio.manze...@fjordforsk.no> To: gmx-users <gmx-us...@gromacs.org> Subject: [gmx-users] Topolgen and topolbuild Message-ID: <1029199322.16738012.1507104624251.javamail.zim...@fjordforsk.no> Content-Type: text/plain; charset=utf-8 Hi, I found these tow programs on GMX site, however they don't work. How can I generate a CHARMM topology to be used in GMX for a charged molecule? Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] Midtun 6894 Vangsnes Norge Org.nr. 911 659 654 Tlf: +47 57695621 [ http://www.oekolab.com/ | ?kolab? ] | [ http://www.nanofact.no/ | Nanofactory? ] | [ http://www.aq-lab.no/ | AQ-Lab? ] | [ http://www.phap.no/ | FAP ] -- 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] Topolgen and topolbuild
Hi Stephane. Thanks for that. I have tried it, however it generates a str file, and from there how to generate the GMX ITP is unknown. Is there a tutorial that shows how to generate ITP from STR? Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] Midtun 6894 Vangsnes Norge Org.nr. 911 659 654 Tlf: +47 57695621 [ http://www.oekolab.com/ | Økolab ] | [ http://www.nanofact.no/ | Nanofactory ] | [ http://www.aq-lab.no/ | AQ-Lab ] | [ http://www.phap.no/ | FAP ] From: "ABEL Stephane" <stephane.a...@cea.fr> To: "gromacs org gmx-users" <gromacs.org_gmx-users@maillist.sys.kth.se> Sent: Wednesday, October 4, 2017 12:15:19 PM Subject: [gmx-users] Topolgen and topolbuild Hi if your molecule is a ligand, you could use ParamChem (https://cgenff.paramchem.org/) Stéphane -- Message: 1 Date: Wed, 4 Oct 2017 10:10:24 +0200 (CEST) From: Sergio Manzetti <sergio.manze...@fjordforsk.no> To: gmx-users <gmx-us...@gromacs.org> Subject: [gmx-users] Topolgen and topolbuild Message-ID: <1029199322.16738012.1507104624251.javamail.zim...@fjordforsk.no> Content-Type: text/plain; charset=utf-8 Hi, I found these tow programs on GMX site, however they don't work. How can I generate a CHARMM topology to be used in GMX for a charged molecule? Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] Midtun 6894 Vangsnes Norge Org.nr. 911 659 654 Tlf: +47 57695621 [ http://www.oekolab.com/ | ?kolab? ] | [ http://www.nanofact.no/ | Nanofactory? ] | [ http://www.aq-lab.no/ | AQ-Lab? ] | [ http://www.phap.no/ | FAP ] -- 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] Topolgen and topolbuild
Hi if your molecule is a ligand, you could use ParamChem (https://cgenff.paramchem.org/) Stéphane -- Message: 1 Date: Wed, 4 Oct 2017 10:10:24 +0200 (CEST) From: Sergio Manzetti <sergio.manze...@fjordforsk.no> To: gmx-users <gmx-us...@gromacs.org> Subject: [gmx-users] Topolgen and topolbuild Message-ID: <1029199322.16738012.1507104624251.javamail.zim...@fjordforsk.no> Content-Type: text/plain; charset=utf-8 Hi, I found these tow programs on GMX site, however they don't work. How can I generate a CHARMM topology to be used in GMX for a charged molecule? Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] Midtun 6894 Vangsnes Norge Org.nr. 911 659 654 Tlf: +47 57695621 [ http://www.oekolab.com/ | ?kolab? ] | [ http://www.nanofact.no/ | Nanofactory? ] | [ http://www.aq-lab.no/ | AQ-Lab? ] | [ http://www.phap.no/ | FAP ] -- 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] Topolgen and topolbuild
Hi, I found these tow programs on GMX site, however they don't work. How can I generate a CHARMM topology to be used in GMX for a charged molecule? Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] Midtun 6894 Vangsnes Norge Org.nr. 911 659 654 Tlf: +47 57695621 [ http://www.oekolab.com/ | Økolab ] | [ http://www.nanofact.no/ | Nanofactory ] | [ http://www.aq-lab.no/ | AQ-Lab ] | [ http://www.phap.no/ | FAP ] -- 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.
