Re: [gmx-users] Topolgen
On 8/18/19 8:44 AM, Bratin Kumar Das wrote: You can use mktop for that...otherwise acpype is also a good option Indeed - TopolGen makes no effort whatsoever to actually parametrize a molecule. It uses known functional groups to try to assign atom types and charges. It relies on known species in OPLS-AA, which are primarily organic. PF6 will not be properly interpreted. -Justin On Sun 18 Aug, 2019, 1:32 PM rakesh parida, wrote: Dear Team, I am new to gromacs software. I have been generating the topology file for the PF6(anion) by using topolgen1.1 software (with the Perl program). The software is generating the skeletal of the .itp file for PF(anion) but there is no bonded parameter in that file. Please suggest me how to generate a complete .itp file for a molecular system. I am giving the .itp file for your reference, which has been generated by topolgen1.1 software. please find it. -- Rakesh Parida Junior Research fellow Department of chemistry, National Institute of Technology, Rourkela -- 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. 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] Topolgen
You can use mktop for that...otherwise acpype is also a good option On Sun 18 Aug, 2019, 1:32 PM rakesh parida, wrote: > Dear Team, > I am new to gromacs software. I have been generating the topology file for > the PF6(anion) by using topolgen1.1 software (with the Perl program). The > software is generating the skeletal of the .itp file for PF(anion) but > there is no bonded parameter in that file. Please suggest me how to > generate a complete .itp file for a molecular system. > I am giving the .itp file for your reference, which has been generated by > topolgen1.1 software. please find it. > > > -- > Rakesh Parida > Junior Research fellow > Department of chemistry, > National Institute of Technology, Rourkela > -- > 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
Dear Team, I am new to gromacs software. I have been generating the topology file for the PF6(anion) by using topolgen1.1 software (with the Perl program). The software is generating the skeletal of the .itp file for PF(anion) but there is no bonded parameter in that file. Please suggest me how to generate a complete .itp file for a molecular system. I am giving the .itp file for your reference, which has been generated by topolgen1.1 software. please find it. -- Rakesh Parida Junior Research fellow Department of chemistry, National Institute of Technology, Rourkela -- 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
Try running this command from the directory where topolgen.pl script is present. On 11/07/2018 09:43, farial tavakoli wrote: Dear gromacs users I am trying to run a simulation on my complex which has small molecule as a ligand , using OPLSAA ff. so I downloaded the topolgen-1.1.tgz and then installed perl script on linux. then typed "perl -v" to check if it is installed. the perl 5.20.1 is installed. but when I typed " perl topolgen.pl -f input.pdb -o output.top [-type itp/top] " command to generate ligand topology , faced with this error: Can't open perl script "topolgen.pl": No such file or directory Is there anyone to help me to figure out this problem? Infact I am new user in generation topology for small molecules using OPLSAA ff. best Farial -- 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
Dear gromacs users I am trying to run a simulation on my complex which has small molecule as a ligand , using OPLSAA ff. so I downloaded the topolgen-1.1.tgz and then installed perl script on linux. then typed "perl -v" to check if it is installed. the perl 5.20.1 is installed. but when I typed " perl topolgen.pl -f input.pdb -o output.top [-type itp/top] " command to generate ligand topology , faced with this error: Can't open perl script "topolgen.pl": No such file or directory Is there anyone to help me to figure out this problem? Infact I am new user in generation topology for small molecules using OPLSAA ff. best Farial -- 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
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" To: "gmx-users" 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.
[gmx-users] Topolgen and topolbuild
Hi Sergio If you have the str file for your molecule, it is straightforward to obtain the itp, since you have all the parameters you need to construct a rtp files. You have to download the charmm ff parameters for gromacs available here http://mackerell.umaryland.edu/~kenno/cgenff/program.php#gromacs http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs Good luck -- Message: 1 Date: Wed, 4 Oct 2017 10:10:24 +0200 (CEST) From: Sergio Manzetti To: gmx-users 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. End of gromacs.org_gmx-users Digest, Vol 162, Issue 12 ** -- 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" To: "gromacs org gmx-users" 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 To: gmx-users 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" To: "gromacs org gmx-users" 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 To: gmx-users 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 To: gmx-users 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.
