Re: [gmx-users] ligand topology building.
On 11/4/19 2:07 AM, Yogesh Sharma wrote: hello users I am using ATB server for ligand topology development. there is a section named FORMAt having options GROMACS, GROMAC11, GROMAC96 and LAMPP what does it mean? and in files section there is choice for Topology Files and structure files as following GROMACS G54A7FF All-Atom (ITP file) GROMACS G54A7FF United-Atom (ITP file) Structure Files All-Atom PDB (optimised geometry) United-Atom PDB (optimised geometry) United-Atom PDB (original geometry) All-Atom PDB (original geometry) what are the best option to proceed with, avoiding artifacts? Is GROMOS a united-atom or all-atom force field? -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] ligand topology building.
hello users I am using ATB server for ligand topology development. there is a section named FORMAt having options GROMACS, GROMAC11, GROMAC96 and LAMPP what does it mean? and in files section there is choice for Topology Files and structure files as following GROMACS G54A7FF All-Atom (ITP file) GROMACS G54A7FF United-Atom (ITP file) Structure Files All-Atom PDB (optimised geometry) United-Atom PDB (optimised geometry) United-Atom PDB (original geometry) All-Atom PDB (original geometry) what are the best option to proceed with, avoiding artifacts? Thank you for your time. * with regards* *Yogesh Sharma* -- 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] ligand topology building
hello users I am using ATB server for ligand topology development. there is a section named FORMAt having options GROMACS, GROMAC11, GROMAC96 and LAMPP what does it mean? and in files section there is choice for Topology Files and structure files as following GROMACS G54A7FF All-Atom (ITP file) GROMACS G54A7FF United-Atom (ITP file) Structure Files All-Atom PDB (optimised geometry) United-Atom PDB (optimised geometry) United-Atom PDB (original geometry) All-Atom PDB (original geometry) what are the best option to proceed with, avoiding artifacts? Thank you for your time. -- 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] ligand topology
I have found However, if one wants *acpype* just to emulate *amb2gmx.pl*, one needs nothing at all but *[http://www.python.org Python]*. At the moment, *acpype* is only available for download via *svn*: * `svn checkout http://acpype.googlecode.com/svn/trunk/ acpype` Yet, if some reason you cannot use *svn*, one still can get *acpype* with: * `wget http://acpype.googlecode.com/svn/trunk/acpype.py` But be aware that one may run in extra troubles and I am not willing to support this way. == To Test == At folder *acpype/test*, type: * `../acpype.py -i FFF.pdb` It'll create a folder called *FFF.acpype*, and inside it one may find topology files for GROMACS and CNS/XPLOR. On Tue, Aug 1, 2017 at 3:00 PM, Mark Abraham wrote: > Hi, > > Have you read the acpype documentation before trying to use it? > > Mark > > On Tue, 1 Aug 2017 23:19 Mohammad Zahidul Hossain Khan < > za.par...@gmail.com> > wrote: > > > Dear Sir > > > > I have just use acpype.py -i OAI.pdb > > I am getting the error: > > ERROR: no 'antechamber' executable! > > ERROR: no 'antechamber' executable... aborting ! > > ==> HINT1: is 'AMBERHOME' or 'ACHOME' environment variable set? > > ==> HINT2: is 'antechamber' in your $PATH? > > What 'which antechamber' in your terminal says? > > 'alias' doesn't work for ACPYPE. > > ACPYPE FAILED: 1 > > Total time of execution: less than a second > > > > I am thinking that I have to install amber. But I dont want to do that. > Is > > there any way that I can create ligand topology for gaff. > > > > > > > > On Tue, Aug 1, 2017 at 11:41 AM, Justin Lemkul wrote: > > > > > > > > > > > On 8/1/17 2:23 PM, Lucio Ricardo Montero Valenzuela wrote: > > > > > >> Ok, you should not mix and match forcefields, ¿but in the case of > > >> AMBER99SB for the protein and gaff for ligand? (TIP3P wáter). > > >> > > > > > > GAFF is compatible with AMBER (by design). My comments were warning > that > > > one should not use AMBER for a protein in concert with GROMOS for a > > ligand. > > > > > > -Justin > > > > > > Best regards. > > >> Lucio Montero. > > >> > > >> Enviado desde Correo para Windows 10 > > >> > > >> De: Alan > > >> Enviado: martes, 1 de agosto de 2017 11:01 a. m. > > >> Para: Gromacs > > >> Asunto: Re: [gmx-users] ligand topology > > >> > > >> Please this GitHub link is totally outdated and not linked in any > sense > > to > > >> the original authors. > > >> > > >> Get the correct ACPYPE here: > > >> > > >> svn checkout http://ccpn.svn.sourceforge.net/svnroot/ccpn/branches/ > > >> stable/ccpn/python/acpype acpype > > >> > > >> On 1 August 2017 at 15:00, Suhaib Shekfeh > wrote: > > >> > > >> Actually, GAFF forcefield and amber forcefields are compatible. gaff > is > > >>> simply amber ff for small molecules. > > >>> You have to get first amber tools. The last release is amber tools 16 > > >>> Get the source code from here : > > >>> http://ambermd.org/AmberTools16-get.html > > >>> > > >>> after installation you can use antechamber for creating the > > >>> small-molecule > > >>> parameters > > >>> > > >>> later, you can use a nice free program called ACEPYP, made to convert > > >>> amber > > >>> parameters to gromacs toplogyget the code from here: > > >>> > > >>> https://github.com/t-/acpype > > >>> > > >>> Regards > > >>> > > >>> > > >>> > > >>> On Tue, Aug 1, 2017 at 1:17 AM, Mohammad Zahidul Hossain Khan < > > >>> za.par...@gmail.com> wrote: > > >>> > > >>> Dear Sir > > >>>> > > >>>> Thank you very much for your reply. Can you give me any link or > > >>>> > > >>> suggestion > > >>> > > >>>> that i can learn for amber force field for protein and ligand. > > >>>> > > >>>> On Mon, Jul 31, 2017 at 3:53 PM, Justin Lemkul > > wrote: > > >>>> > > >>>> > > >>>>> > > >>>>> On 7/31/17 2:42 PM, Mohammad Zahidul
Re: [gmx-users] ligand topology
Hi, Have you read the acpype documentation before trying to use it? Mark On Tue, 1 Aug 2017 23:19 Mohammad Zahidul Hossain Khan wrote: > Dear Sir > > I have just use acpype.py -i OAI.pdb > I am getting the error: > ERROR: no 'antechamber' executable! > ERROR: no 'antechamber' executable... aborting ! > ==> HINT1: is 'AMBERHOME' or 'ACHOME' environment variable set? > ==> HINT2: is 'antechamber' in your $PATH? > What 'which antechamber' in your terminal says? > 'alias' doesn't work for ACPYPE. > ACPYPE FAILED: 1 > Total time of execution: less than a second > > I am thinking that I have to install amber. But I dont want to do that. Is > there any way that I can create ligand topology for gaff. > > > > On Tue, Aug 1, 2017 at 11:41 AM, Justin Lemkul wrote: > > > > > > > On 8/1/17 2:23 PM, Lucio Ricardo Montero Valenzuela wrote: > > > >> Ok, you should not mix and match forcefields, ¿but in the case of > >> AMBER99SB for the protein and gaff for ligand? (TIP3P wáter). > >> > > > > GAFF is compatible with AMBER (by design). My comments were warning that > > one should not use AMBER for a protein in concert with GROMOS for a > ligand. > > > > -Justin > > > > Best regards. > >> Lucio Montero. > >> > >> Enviado desde Correo para Windows 10 > >> > >> De: Alan > >> Enviado: martes, 1 de agosto de 2017 11:01 a. m. > >> Para: Gromacs > >> Asunto: Re: [gmx-users] ligand topology > >> > >> Please this GitHub link is totally outdated and not linked in any sense > to > >> the original authors. > >> > >> Get the correct ACPYPE here: > >> > >> svn checkout http://ccpn.svn.sourceforge.net/svnroot/ccpn/branches/ > >> stable/ccpn/python/acpype acpype > >> > >> On 1 August 2017 at 15:00, Suhaib Shekfeh wrote: > >> > >> Actually, GAFF forcefield and amber forcefields are compatible. gaff is > >>> simply amber ff for small molecules. > >>> You have to get first amber tools. The last release is amber tools 16 > >>> Get the source code from here : > >>> http://ambermd.org/AmberTools16-get.html > >>> > >>> after installation you can use antechamber for creating the > >>> small-molecule > >>> parameters > >>> > >>> later, you can use a nice free program called ACEPYP, made to convert > >>> amber > >>> parameters to gromacs toplogyget the code from here: > >>> > >>> https://github.com/t-/acpype > >>> > >>> Regards > >>> > >>> > >>> > >>> On Tue, Aug 1, 2017 at 1:17 AM, Mohammad Zahidul Hossain Khan < > >>> za.par...@gmail.com> wrote: > >>> > >>> Dear Sir > >>>> > >>>> Thank you very much for your reply. Can you give me any link or > >>>> > >>> suggestion > >>> > >>>> that i can learn for amber force field for protein and ligand. > >>>> > >>>> On Mon, Jul 31, 2017 at 3:53 PM, Justin Lemkul > wrote: > >>>> > >>>> > >>>>> > >>>>> On 7/31/17 2:42 PM, Mohammad Zahidul Hossain Khan wrote: > >>>>> > >>>>> Dear Sir > >>>>>> > >>>>>> I am new for protein-ligand complex. I want amber force field (ff03) > >>>>>> > >>>>> for > >>> > >>>> my > >>>>>> protein, tip3p for water model and gaff (General Amber force field) > >>>>>> > >>>>> for > >>> > >>>> ligand. I do not know how to produce gaff force field from pdb and > >>>>>> > >>>>> then > >>> > >>>> convert for gromacs topology. > >>>>>> > >>>>>> I have tried ff03 with gromos ligand topology and tip3p water model > >>>>>> > >>>>>> it gives me the error: > >>>>>> atomtype OM not found > >>>>>> > >>>>>> and when I have tried ff03 with gromos topology and spc water model > it > >>>>>> gives me the error like: > >>>>>> atomtype HW not found. > >>>>>> > >>>>>> Can anyo
Re: [gmx-users] ligand topology
http://webapps.ccpn.ac.uk/acpype/ On 1 August 2017 at 22:18, Mohammad Zahidul Hossain Khan < za.par...@gmail.com> wrote: > Dear Sir > > I have just use acpype.py -i OAI.pdb > I am getting the error: > ERROR: no 'antechamber' executable! > ERROR: no 'antechamber' executable... aborting ! > ==> HINT1: is 'AMBERHOME' or 'ACHOME' environment variable set? > ==> HINT2: is 'antechamber' in your $PATH? > What 'which antechamber' in your terminal says? > 'alias' doesn't work for ACPYPE. > ACPYPE FAILED: 1 > Total time of execution: less than a second > > I am thinking that I have to install amber. But I dont want to do that. Is > there any way that I can create ligand topology for gaff. > > > > On Tue, Aug 1, 2017 at 11:41 AM, Justin Lemkul wrote: > > > > > > > On 8/1/17 2:23 PM, Lucio Ricardo Montero Valenzuela wrote: > > > >> Ok, you should not mix and match forcefields, ¿but in the case of > >> AMBER99SB for the protein and gaff for ligand? (TIP3P wáter). > >> > > > > GAFF is compatible with AMBER (by design). My comments were warning that > > one should not use AMBER for a protein in concert with GROMOS for a > ligand. > > > > -Justin > > > > Best regards. > >> Lucio Montero. > >> > >> Enviado desde Correo para Windows 10 > >> > >> De: Alan > >> Enviado: martes, 1 de agosto de 2017 11:01 a. m. > >> Para: Gromacs > >> Asunto: Re: [gmx-users] ligand topology > >> > >> Please this GitHub link is totally outdated and not linked in any sense > to > >> the original authors. > >> > >> Get the correct ACPYPE here: > >> > >> svn checkout http://ccpn.svn.sourceforge.net/svnroot/ccpn/branches/ > >> stable/ccpn/python/acpype acpype > >> > >> On 1 August 2017 at 15:00, Suhaib Shekfeh wrote: > >> > >> Actually, GAFF forcefield and amber forcefields are compatible. gaff is > >>> simply amber ff for small molecules. > >>> You have to get first amber tools. The last release is amber tools 16 > >>> Get the source code from here : > >>> http://ambermd.org/AmberTools16-get.html > >>> > >>> after installation you can use antechamber for creating the > >>> small-molecule > >>> parameters > >>> > >>> later, you can use a nice free program called ACEPYP, made to convert > >>> amber > >>> parameters to gromacs toplogyget the code from here: > >>> > >>> https://github.com/t-/acpype > >>> > >>> Regards > >>> > >>> > >>> > >>> On Tue, Aug 1, 2017 at 1:17 AM, Mohammad Zahidul Hossain Khan < > >>> za.par...@gmail.com> wrote: > >>> > >>> Dear Sir > >>>> > >>>> Thank you very much for your reply. Can you give me any link or > >>>> > >>> suggestion > >>> > >>>> that i can learn for amber force field for protein and ligand. > >>>> > >>>> On Mon, Jul 31, 2017 at 3:53 PM, Justin Lemkul > wrote: > >>>> > >>>> > >>>>> > >>>>> On 7/31/17 2:42 PM, Mohammad Zahidul Hossain Khan wrote: > >>>>> > >>>>> Dear Sir > >>>>>> > >>>>>> I am new for protein-ligand complex. I want amber force field (ff03) > >>>>>> > >>>>> for > >>> > >>>> my > >>>>>> protein, tip3p for water model and gaff (General Amber force field) > >>>>>> > >>>>> for > >>> > >>>> ligand. I do not know how to produce gaff force field from pdb and > >>>>>> > >>>>> then > >>> > >>>> convert for gromacs topology. > >>>>>> > >>>>>> I have tried ff03 with gromos ligand topology and tip3p water model > >>>>>> > >>>>>> it gives me the error: > >>>>>> atomtype OM not found > >>>>>> > >>>>>> and when I have tried ff03 with gromos topology and spc water model > it > >>>>>> gives me the error like: > >>>>>> atomtype HW not found. > >>>>>> > >>>>>> Ca
Re: [gmx-users] ligand topology
Dear Sir I have just use acpype.py -i OAI.pdb I am getting the error: ERROR: no 'antechamber' executable! ERROR: no 'antechamber' executable... aborting ! ==> HINT1: is 'AMBERHOME' or 'ACHOME' environment variable set? ==> HINT2: is 'antechamber' in your $PATH? What 'which antechamber' in your terminal says? 'alias' doesn't work for ACPYPE. ACPYPE FAILED: 1 Total time of execution: less than a second I am thinking that I have to install amber. But I dont want to do that. Is there any way that I can create ligand topology for gaff. On Tue, Aug 1, 2017 at 11:41 AM, Justin Lemkul wrote: > > > On 8/1/17 2:23 PM, Lucio Ricardo Montero Valenzuela wrote: > >> Ok, you should not mix and match forcefields, ¿but in the case of >> AMBER99SB for the protein and gaff for ligand? (TIP3P wáter). >> > > GAFF is compatible with AMBER (by design). My comments were warning that > one should not use AMBER for a protein in concert with GROMOS for a ligand. > > -Justin > > Best regards. >> Lucio Montero. >> >> Enviado desde Correo para Windows 10 >> >> De: Alan >> Enviado: martes, 1 de agosto de 2017 11:01 a. m. >> Para: Gromacs >> Asunto: Re: [gmx-users] ligand topology >> >> Please this GitHub link is totally outdated and not linked in any sense to >> the original authors. >> >> Get the correct ACPYPE here: >> >> svn checkout http://ccpn.svn.sourceforge.net/svnroot/ccpn/branches/ >> stable/ccpn/python/acpype acpype >> >> On 1 August 2017 at 15:00, Suhaib Shekfeh wrote: >> >> Actually, GAFF forcefield and amber forcefields are compatible. gaff is >>> simply amber ff for small molecules. >>> You have to get first amber tools. The last release is amber tools 16 >>> Get the source code from here : >>> http://ambermd.org/AmberTools16-get.html >>> >>> after installation you can use antechamber for creating the >>> small-molecule >>> parameters >>> >>> later, you can use a nice free program called ACEPYP, made to convert >>> amber >>> parameters to gromacs toplogyget the code from here: >>> >>> https://github.com/t-/acpype >>> >>> Regards >>> >>> >>> >>> On Tue, Aug 1, 2017 at 1:17 AM, Mohammad Zahidul Hossain Khan < >>> za.par...@gmail.com> wrote: >>> >>> Dear Sir >>>> >>>> Thank you very much for your reply. Can you give me any link or >>>> >>> suggestion >>> >>>> that i can learn for amber force field for protein and ligand. >>>> >>>> On Mon, Jul 31, 2017 at 3:53 PM, Justin Lemkul wrote: >>>> >>>> >>>>> >>>>> On 7/31/17 2:42 PM, Mohammad Zahidul Hossain Khan wrote: >>>>> >>>>> Dear Sir >>>>>> >>>>>> I am new for protein-ligand complex. I want amber force field (ff03) >>>>>> >>>>> for >>> >>>> my >>>>>> protein, tip3p for water model and gaff (General Amber force field) >>>>>> >>>>> for >>> >>>> ligand. I do not know how to produce gaff force field from pdb and >>>>>> >>>>> then >>> >>>> convert for gromacs topology. >>>>>> >>>>>> I have tried ff03 with gromos ligand topology and tip3p water model >>>>>> >>>>>> it gives me the error: >>>>>> atomtype OM not found >>>>>> >>>>>> and when I have tried ff03 with gromos topology and spc water model it >>>>>> gives me the error like: >>>>>> atomtype HW not found. >>>>>> >>>>>> Can anyone help me about it? >>>>>> >>>>>> >>>>>> You can't mix and match force fields; it's fundamentally wrong. You >>>>> >>>> need >>> >>>> to develop ligand parameters that are consistent with the parent >>>>> >>>> protein >>> >>>> force field. Various tools exist for different force fields, with >>>>> >>>> varying >>>> >>>>> degrees of reliability. >>>>> >>>>> -Justin >>>>> >>>>> -- >>>>> == >>>>> >>>&g
Re: [gmx-users] ligand topology
On 8/1/17 2:23 PM, Lucio Ricardo Montero Valenzuela wrote: Ok, you should not mix and match forcefields, ¿but in the case of AMBER99SB for the protein and gaff for ligand? (TIP3P wáter). GAFF is compatible with AMBER (by design). My comments were warning that one should not use AMBER for a protein in concert with GROMOS for a ligand. -Justin Best regards. Lucio Montero. Enviado desde Correo para Windows 10 De: Alan Enviado: martes, 1 de agosto de 2017 11:01 a. m. Para: Gromacs Asunto: Re: [gmx-users] ligand topology Please this GitHub link is totally outdated and not linked in any sense to the original authors. Get the correct ACPYPE here: svn checkout http://ccpn.svn.sourceforge.net/svnroot/ccpn/branches/ stable/ccpn/python/acpype acpype On 1 August 2017 at 15:00, Suhaib Shekfeh wrote: Actually, GAFF forcefield and amber forcefields are compatible. gaff is simply amber ff for small molecules. You have to get first amber tools. The last release is amber tools 16 Get the source code from here : http://ambermd.org/AmberTools16-get.html after installation you can use antechamber for creating the small-molecule parameters later, you can use a nice free program called ACEPYP, made to convert amber parameters to gromacs toplogyget the code from here: https://github.com/t-/acpype Regards On Tue, Aug 1, 2017 at 1:17 AM, Mohammad Zahidul Hossain Khan < za.par...@gmail.com> wrote: Dear Sir Thank you very much for your reply. Can you give me any link or suggestion that i can learn for amber force field for protein and ligand. On Mon, Jul 31, 2017 at 3:53 PM, Justin Lemkul wrote: On 7/31/17 2:42 PM, Mohammad Zahidul Hossain Khan wrote: Dear Sir I am new for protein-ligand complex. I want amber force field (ff03) for my protein, tip3p for water model and gaff (General Amber force field) for ligand. I do not know how to produce gaff force field from pdb and then convert for gromacs topology. I have tried ff03 with gromos ligand topology and tip3p water model it gives me the error: atomtype OM not found and when I have tried ff03 with gromos topology and spc water model it gives me the error like: atomtype HW not found. Can anyone help me about it? You can't mix and match force fields; it's fundamentally wrong. You need to develop ligand parameters that are consistent with the parent protein force field. Various tools exist for different force fields, with varying degrees of reliability. -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. -- *Mohammad Zahidul Hossain Khan Graduate student**Department of Physics* *Email: khan5...@vandals.uidaho.edu * * Skype: parash.khan2* *Cell: +12085967165* -- 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. -- Dr. rer. nat. Suhaib Shekfeh PhD in Computational Drug Design and Medicinal Chemistry Oleariusstr. 11, Halle (Saale), Germany LinkedIn : http://www.linkedin.com/pub/suhaib-shekfeh/b/65a/255 -- 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://w
Re: [gmx-users] ligand topology
Ok, you should not mix and match forcefields, ¿but in the case of AMBER99SB for the protein and gaff for ligand? (TIP3P wáter). Best regards. Lucio Montero. Enviado desde Correo para Windows 10 De: Alan Enviado: martes, 1 de agosto de 2017 11:01 a. m. Para: Gromacs Asunto: Re: [gmx-users] ligand topology Please this GitHub link is totally outdated and not linked in any sense to the original authors. Get the correct ACPYPE here: svn checkout http://ccpn.svn.sourceforge.net/svnroot/ccpn/branches/ stable/ccpn/python/acpype acpype On 1 August 2017 at 15:00, Suhaib Shekfeh wrote: > Actually, GAFF forcefield and amber forcefields are compatible. gaff is > simply amber ff for small molecules. > You have to get first amber tools. The last release is amber tools 16 > Get the source code from here : > http://ambermd.org/AmberTools16-get.html > > after installation you can use antechamber for creating the small-molecule > parameters > > later, you can use a nice free program called ACEPYP, made to convert amber > parameters to gromacs toplogyget the code from here: > > https://github.com/t-/acpype > > Regards > > > > On Tue, Aug 1, 2017 at 1:17 AM, Mohammad Zahidul Hossain Khan < > za.par...@gmail.com> wrote: > > > Dear Sir > > > > Thank you very much for your reply. Can you give me any link or > suggestion > > that i can learn for amber force field for protein and ligand. > > > > On Mon, Jul 31, 2017 at 3:53 PM, Justin Lemkul wrote: > > > > > > > > > > > On 7/31/17 2:42 PM, Mohammad Zahidul Hossain Khan wrote: > > > > > >> Dear Sir > > >> > > >> I am new for protein-ligand complex. I want amber force field (ff03) > for > > >> my > > >> protein, tip3p for water model and gaff (General Amber force field) > for > > >> ligand. I do not know how to produce gaff force field from pdb and > then > > >> convert for gromacs topology. > > >> > > >> I have tried ff03 with gromos ligand topology and tip3p water model > > >> > > >> it gives me the error: > > >> atomtype OM not found > > >> > > >> and when I have tried ff03 with gromos topology and spc water model it > > >> gives me the error like: > > >> atomtype HW not found. > > >> > > >> Can anyone help me about it? > > >> > > >> > > > You can't mix and match force fields; it's fundamentally wrong. You > need > > > to develop ligand parameters that are consistent with the parent > protein > > > force field. Various tools exist for different force fields, with > > varying > > > degrees of reliability. > > > > > > -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. > > > > > > > > > > > -- > > > > > > *Mohammad Zahidul Hossain Khan Graduate student**Department of Physics* > > *Email: khan5...@vandals.uidaho.edu * > > * Skype: parash.khan2* > > *Cell: +12085967165* > > -- > > 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. > > > > > > -- > Dr. rer. nat. S
Re: [gmx-users] ligand topology
Dear Sir Thank you very much. On Tue, Aug 1, 2017 at 7:00 AM, Suhaib Shekfeh wrote: > Actually, GAFF forcefield and amber forcefields are compatible. gaff is > simply amber ff for small molecules. > You have to get first amber tools. The last release is amber tools 16 > Get the source code from here : > http://ambermd.org/AmberTools16-get.html > > after installation you can use antechamber for creating the small-molecule > parameters > > later, you can use a nice free program called ACEPYP, made to convert amber > parameters to gromacs toplogyget the code from here: > > https://github.com/t-/acpype > > Regards > > > > On Tue, Aug 1, 2017 at 1:17 AM, Mohammad Zahidul Hossain Khan < > za.par...@gmail.com> wrote: > > > Dear Sir > > > > Thank you very much for your reply. Can you give me any link or > suggestion > > that i can learn for amber force field for protein and ligand. > > > > On Mon, Jul 31, 2017 at 3:53 PM, Justin Lemkul wrote: > > > > > > > > > > > On 7/31/17 2:42 PM, Mohammad Zahidul Hossain Khan wrote: > > > > > >> Dear Sir > > >> > > >> I am new for protein-ligand complex. I want amber force field (ff03) > for > > >> my > > >> protein, tip3p for water model and gaff (General Amber force field) > for > > >> ligand. I do not know how to produce gaff force field from pdb and > then > > >> convert for gromacs topology. > > >> > > >> I have tried ff03 with gromos ligand topology and tip3p water model > > >> > > >> it gives me the error: > > >> atomtype OM not found > > >> > > >> and when I have tried ff03 with gromos topology and spc water model it > > >> gives me the error like: > > >> atomtype HW not found. > > >> > > >> Can anyone help me about it? > > >> > > >> > > > You can't mix and match force fields; it's fundamentally wrong. You > need > > > to develop ligand parameters that are consistent with the parent > protein > > > force field. Various tools exist for different force fields, with > > varying > > > degrees of reliability. > > > > > > -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. > > > > > > > > > > > -- > > > > > > *Mohammad Zahidul Hossain Khan Graduate student**Department of Physics* > > *Email: khan5...@vandals.uidaho.edu * > > * Skype: parash.khan2* > > *Cell: +12085967165* > > -- > > 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. > > > > > > -- > Dr. rer. nat. Suhaib Shekfeh > PhD in Computational Drug Design and Medicinal Chemistry > Oleariusstr. 11, Halle (Saale), Germany > LinkedIn : http://www.linkedin.com/pub/suhaib-shekfeh/b/65a/255 > -- > 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. > -- *Mohammad Zahidul Hossain Khan Graduate student**Department of Physics* *Email: khan5...@vandals.uidaho.edu * * Skype: parash.khan2* *Cell: +12085967165* -- 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] ligand topology
Please this GitHub link is totally outdated and not linked in any sense to the original authors. Get the correct ACPYPE here: svn checkout http://ccpn.svn.sourceforge.net/svnroot/ccpn/branches/ stable/ccpn/python/acpype acpype On 1 August 2017 at 15:00, Suhaib Shekfeh wrote: > Actually, GAFF forcefield and amber forcefields are compatible. gaff is > simply amber ff for small molecules. > You have to get first amber tools. The last release is amber tools 16 > Get the source code from here : > http://ambermd.org/AmberTools16-get.html > > after installation you can use antechamber for creating the small-molecule > parameters > > later, you can use a nice free program called ACEPYP, made to convert amber > parameters to gromacs toplogyget the code from here: > > https://github.com/t-/acpype > > Regards > > > > On Tue, Aug 1, 2017 at 1:17 AM, Mohammad Zahidul Hossain Khan < > za.par...@gmail.com> wrote: > > > Dear Sir > > > > Thank you very much for your reply. Can you give me any link or > suggestion > > that i can learn for amber force field for protein and ligand. > > > > On Mon, Jul 31, 2017 at 3:53 PM, Justin Lemkul wrote: > > > > > > > > > > > On 7/31/17 2:42 PM, Mohammad Zahidul Hossain Khan wrote: > > > > > >> Dear Sir > > >> > > >> I am new for protein-ligand complex. I want amber force field (ff03) > for > > >> my > > >> protein, tip3p for water model and gaff (General Amber force field) > for > > >> ligand. I do not know how to produce gaff force field from pdb and > then > > >> convert for gromacs topology. > > >> > > >> I have tried ff03 with gromos ligand topology and tip3p water model > > >> > > >> it gives me the error: > > >> atomtype OM not found > > >> > > >> and when I have tried ff03 with gromos topology and spc water model it > > >> gives me the error like: > > >> atomtype HW not found. > > >> > > >> Can anyone help me about it? > > >> > > >> > > > You can't mix and match force fields; it's fundamentally wrong. You > need > > > to develop ligand parameters that are consistent with the parent > protein > > > force field. Various tools exist for different force fields, with > > varying > > > degrees of reliability. > > > > > > -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. > > > > > > > > > > > -- > > > > > > *Mohammad Zahidul Hossain Khan Graduate student**Department of Physics* > > *Email: khan5...@vandals.uidaho.edu * > > * Skype: parash.khan2* > > *Cell: +12085967165* > > -- > > 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. > > > > > > -- > Dr. rer. nat. Suhaib Shekfeh > PhD in Computational Drug Design and Medicinal Chemistry > Oleariusstr. 11, Halle (Saale), Germany > LinkedIn : http://www.linkedin.com/pub/suhaib-shekfeh/b/65a/255 > -- > 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] ligand topology
Actually, GAFF forcefield and amber forcefields are compatible. gaff is simply amber ff for small molecules. You have to get first amber tools. The last release is amber tools 16 Get the source code from here : http://ambermd.org/AmberTools16-get.html after installation you can use antechamber for creating the small-molecule parameters later, you can use a nice free program called ACEPYP, made to convert amber parameters to gromacs toplogyget the code from here: https://github.com/t-/acpype Regards On Tue, Aug 1, 2017 at 1:17 AM, Mohammad Zahidul Hossain Khan < za.par...@gmail.com> wrote: > Dear Sir > > Thank you very much for your reply. Can you give me any link or suggestion > that i can learn for amber force field for protein and ligand. > > On Mon, Jul 31, 2017 at 3:53 PM, Justin Lemkul wrote: > > > > > > > On 7/31/17 2:42 PM, Mohammad Zahidul Hossain Khan wrote: > > > >> Dear Sir > >> > >> I am new for protein-ligand complex. I want amber force field (ff03) for > >> my > >> protein, tip3p for water model and gaff (General Amber force field) for > >> ligand. I do not know how to produce gaff force field from pdb and then > >> convert for gromacs topology. > >> > >> I have tried ff03 with gromos ligand topology and tip3p water model > >> > >> it gives me the error: > >> atomtype OM not found > >> > >> and when I have tried ff03 with gromos topology and spc water model it > >> gives me the error like: > >> atomtype HW not found. > >> > >> Can anyone help me about it? > >> > >> > > You can't mix and match force fields; it's fundamentally wrong. You need > > to develop ligand parameters that are consistent with the parent protein > > force field. Various tools exist for different force fields, with > varying > > degrees of reliability. > > > > -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. > > > > > > -- > > > *Mohammad Zahidul Hossain Khan Graduate student**Department of Physics* > *Email: khan5...@vandals.uidaho.edu * > * Skype: parash.khan2* > *Cell: +12085967165* > -- > 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. > -- Dr. rer. nat. Suhaib Shekfeh PhD in Computational Drug Design and Medicinal Chemistry Oleariusstr. 11, Halle (Saale), Germany LinkedIn : http://www.linkedin.com/pub/suhaib-shekfeh/b/65a/255 -- 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] ligand topology
Dear Sir Thank you very much for your reply. Can you give me any link or suggestion that i can learn for amber force field for protein and ligand. On Mon, Jul 31, 2017 at 3:53 PM, Justin Lemkul wrote: > > > On 7/31/17 2:42 PM, Mohammad Zahidul Hossain Khan wrote: > >> Dear Sir >> >> I am new for protein-ligand complex. I want amber force field (ff03) for >> my >> protein, tip3p for water model and gaff (General Amber force field) for >> ligand. I do not know how to produce gaff force field from pdb and then >> convert for gromacs topology. >> >> I have tried ff03 with gromos ligand topology and tip3p water model >> >> it gives me the error: >> atomtype OM not found >> >> and when I have tried ff03 with gromos topology and spc water model it >> gives me the error like: >> atomtype HW not found. >> >> Can anyone help me about it? >> >> > You can't mix and match force fields; it's fundamentally wrong. You need > to develop ligand parameters that are consistent with the parent protein > force field. Various tools exist for different force fields, with varying > degrees of reliability. > > -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. > -- *Mohammad Zahidul Hossain Khan Graduate student**Department of Physics* *Email: khan5...@vandals.uidaho.edu * * Skype: parash.khan2* *Cell: +12085967165* -- 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] ligand topology
On 7/31/17 2:42 PM, Mohammad Zahidul Hossain Khan wrote: Dear Sir I am new for protein-ligand complex. I want amber force field (ff03) for my protein, tip3p for water model and gaff (General Amber force field) for ligand. I do not know how to produce gaff force field from pdb and then convert for gromacs topology. I have tried ff03 with gromos ligand topology and tip3p water model it gives me the error: atomtype OM not found and when I have tried ff03 with gromos topology and spc water model it gives me the error like: atomtype HW not found. Can anyone help me about it? You can't mix and match force fields; it's fundamentally wrong. You need to develop ligand parameters that are consistent with the parent protein force field. Various tools exist for different force fields, with varying degrees of reliability. -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] ligand topology
Dear Sir I am new for protein-ligand complex. I want amber force field (ff03) for my protein, tip3p for water model and gaff (General Amber force field) for ligand. I do not know how to produce gaff force field from pdb and then convert for gromacs topology. I have tried ff03 with gromos ligand topology and tip3p water model it gives me the error: atomtype OM not found and when I have tried ff03 with gromos topology and spc water model it gives me the error like: atomtype HW not found. Can anyone help me about it? -- *Mohammad Zahidul Hossain Khan Graduate student**Department of Physics* *Email: khan5...@vandals.uidaho.edu * * Skype: parash.khan2* *Cell: +12085967165* -- 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] Ligand topology
blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px
#715FFA solid !important; padding-left:1ex !important; background-color:white
!important; } Dear gromacs users
Is there any way to create ligand topology file by using pdb2gmx instead of
prodrg? Because i use gromos 43a1 ff for making protein topology and use prodrg
to create ligand topoligy and .gro file. But i dont know anything about
reparametrizing the ligand topology but reassigning charge and charge groups.
Is there anyone can help me:1) is it possible to make ligand topology file by
pdb2gmx 2) what kind of reparametrizations are needed to be done to obtain the
proper ligand topol.top file but reassigning charges and charge groups that
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Re: [gmx-users] Ligand topology
Hi, The run will be slightly slower with the restraints. But more significant will be the further equilibration time to start to sample the unrestrained ensemble. Mark On Thu, 30 Mar 2017 12:26 RAHUL SURESH wrote: > I am running NVT Equilibration for Protein_ligand complex as per the the > tutorial. > > Will time consumption for equilibration increase in applying position > restrains for both ligand and protein? > > -- > *Regards,* > *Rahul Suresh* > *Research Scholar* > *Bharathiar University* > *Coimbatore* > -- > 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] Ligand topology
I am running NVT Equilibration for Protein_ligand complex as per the the tutorial. Will time consumption for equilibration increase in applying position restrains for both ligand and protein? -- *Regards,* *Rahul Suresh* *Research Scholar* *Bharathiar University* *Coimbatore* -- 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] ligand topology & charge calculations
Can somebody suggest what could be the best possible way for generating small molecules topology file and charge determination ( OPLS force field) as I want carry out a simulation for miscell formation between small ligands. -- 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] Ligand Topology file
On 1/27/15 3:41 AM, neha bharti wrote: Hello All I am performing Molecular dynamics simulation of protein and ligand complex. I am using GROMOS96 53a6 force field. For Ligand topology file I am using Automated topology builder. In the grompp step ( grompp -f ion.mdp -c solv.gro -p topol.top -o ions.tpr) when I tried to add ion it gives me Note that NOTE 2 [file topol.top]: The largest charge group contains 14 atoms. Since atoms only see each other when the centers of geometry of the charge groups they belong to are within the cut-off distance, too large charge groups can lead to serious cut-off artifacts. For efficiency and accuracy, charge group should consist of a few atoms. For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc. Following is the atom charge group of .itp file which I get from Automated topology builder [ atoms ] ; nr type resnr resid atom cgnr chargemasstotal_charge 1 C 16P5PC151 -0.050 12.0110 2 C 16P5PC1610.023 12.0110 3 C 16P5PC1710.023 12.0110 4 C 16P5PC181 -0.050 12.0110 5 C 16P5PC1910.023 12.0110 6 C 16P5PC2010.023 12.0110 7 C 16P5PC1410.580 12.0110 8 O 16P5P O1 1 -0.571 15.9994 9 C 16P5PC2110.570 12.0110 10 O 16P5P O21 -0.571 15.9994 ; 0.000 11 N 16P5P N32 -0.486 14.0067 12 H 16P5PH1120.486 1.0080 ; 0.000 13 C 16P5PC1230.251 12.0110 14 C 16P5PC113 -0.019 12.0110 15 C 16P5PC103 -0.070 12.0110 16 C 16P5P C930.089 12.0110 17 C 16P5P C83 -0.185 12.0110 18 C 16P5PC133 -0.089 12.0110 19 C 16P5P C730.491 12.0110 20NR16P5P N23 -0.468 14.0067 ; -0.000 21NR16P5P N14 -0.365 14.0067 22 H 16P5P H140.365 1.0080 ; 0.000 23 C 16P5P C550.155 12.0110 24 C 16P5P C450.115 12.0110 25 C 16P5P C65 -0.042 12.0110 26 C 16P5P C35 -0.042 12.0110 27 C 16P5P C25 -0.093 12.0110 28 C 16P5P C15 -0.093 12.0110 ; 0.000 29 N 16P5P N46 -0.486 14.0067 30 H 16P5PH1660.486 1.0080 ; 0.000 31 C 16P5PC2270.240 12.0110 32 C 16P5PC277 -0.100 12.0110 33 C 16P5PC267 -0.196 12.0110 34 C 16P5PC2570.078 12.0110 35 C 16P5PC247 -0.081 12.0110 36 C 16P5PC237 -0.030 12.0110 37 C 16P5PC2870.478 12.0110 38NR16P5P N67 -0.475 14.0067 39 C 16P5PC3470.138 12.0110 40 C 16P5PC2970.170 12.0110 41 C 16P5PC337 -0.030 12.0110 42 C 16P5PC307 -0.030 12.0110 43 C 16P5PC317 -0.081 12.0110 44 C 16P5PC327 -0.081 12.0110 ; 0.000 45NR16P5P N58 -0.365 14.0067 46 H 16P5P H280.365 1.0080 ; 0.000 ; total charge of the molecule: -0.000 Should I ignore the error or is there something wrong in my charge group generated from ATB. Can any one please help me out to solve the problem. There are several charge groups that are too large, and group 7 is the one that is triggering the problem. Note that charge groups are only relevant for the group cutoff scheme, and are ignored with Verlet. Scrutinize all elements of the topology; if something as fundamental as the charge groups (which should only ever encompass 2-4 atoms based on chemical moiety) are this bizarre, likely the charges are suboptimal, as well. -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 == -- G
[gmx-users] Ligand Topology file
Hello All I am performing Molecular dynamics simulation of protein and ligand complex. I am using GROMOS96 53a6 force field. For Ligand topology file I am using Automated topology builder. In the grompp step ( grompp -f ion.mdp -c solv.gro -p topol.top -o ions.tpr) when I tried to add ion it gives me Note that NOTE 2 [file topol.top]: The largest charge group contains 14 atoms. Since atoms only see each other when the centers of geometry of the charge groups they belong to are within the cut-off distance, too large charge groups can lead to serious cut-off artifacts. For efficiency and accuracy, charge group should consist of a few atoms. For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc. Following is the atom charge group of .itp file which I get from Automated topology builder [ atoms ] ; nr type resnr resid atom cgnr chargemasstotal_charge 1 C 16P5PC151 -0.050 12.0110 2 C 16P5PC1610.023 12.0110 3 C 16P5PC1710.023 12.0110 4 C 16P5PC181 -0.050 12.0110 5 C 16P5PC1910.023 12.0110 6 C 16P5PC2010.023 12.0110 7 C 16P5PC1410.580 12.0110 8 O 16P5P O1 1 -0.571 15.9994 9 C 16P5PC2110.570 12.0110 10 O 16P5P O21 -0.571 15.9994 ; 0.000 11 N 16P5P N32 -0.486 14.0067 12 H 16P5PH1120.486 1.0080 ; 0.000 13 C 16P5PC1230.251 12.0110 14 C 16P5PC113 -0.019 12.0110 15 C 16P5PC103 -0.070 12.0110 16 C 16P5P C930.089 12.0110 17 C 16P5P C83 -0.185 12.0110 18 C 16P5PC133 -0.089 12.0110 19 C 16P5P C730.491 12.0110 20NR16P5P N23 -0.468 14.0067 ; -0.000 21NR16P5P N14 -0.365 14.0067 22 H 16P5P H140.365 1.0080 ; 0.000 23 C 16P5P C550.155 12.0110 24 C 16P5P C450.115 12.0110 25 C 16P5P C65 -0.042 12.0110 26 C 16P5P C35 -0.042 12.0110 27 C 16P5P C25 -0.093 12.0110 28 C 16P5P C15 -0.093 12.0110 ; 0.000 29 N 16P5P N46 -0.486 14.0067 30 H 16P5PH1660.486 1.0080 ; 0.000 31 C 16P5PC2270.240 12.0110 32 C 16P5PC277 -0.100 12.0110 33 C 16P5PC267 -0.196 12.0110 34 C 16P5PC2570.078 12.0110 35 C 16P5PC247 -0.081 12.0110 36 C 16P5PC237 -0.030 12.0110 37 C 16P5PC2870.478 12.0110 38NR16P5P N67 -0.475 14.0067 39 C 16P5PC3470.138 12.0110 40 C 16P5PC2970.170 12.0110 41 C 16P5PC337 -0.030 12.0110 42 C 16P5PC307 -0.030 12.0110 43 C 16P5PC317 -0.081 12.0110 44 C 16P5PC327 -0.081 12.0110 ; 0.000 45NR16P5P N58 -0.365 14.0067 46 H 16P5P H280.365 1.0080 ; 0.000 ; total charge of the molecule: -0.000 Should I ignore the error or is there something wrong in my charge group generated from ATB. Can any one please help me out to solve the problem. Thanks You. With Regards Neha Bharti -- 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] ligand topology for opls.aa
Пересылаемое сообщение От кого: Andrey Frolov Кому: gromacs.org_gmx-users@maillist.sys.kth.se Копия: samanshahriy...@yahoo.com Дата: Fri, 13 Jun 2014 14:34:50 +0400 Тема: Re: gromacs.org_gmx-users Digest, Vol 122, Issue 61 Dear Saman, You might want to consider OPLS-AA 2005 as implemented in the Shorodinger software. The Schrodinger Maestro is FREE for academia, after registering you can download it and use. There is an utility "ffld_server", which is able to automatically assign OPLS-AA 2005 to any ligand molecule. Once you have the output of ffld_server, you can convert this into gromacs topology format by a python program called "ffconv.py" (see http://frolov-pchem.wikispaces.com/Downloads ). Also you can check if the conversion in your case was correct by "check_conversion.sh" script therein. This is well-documented and has real-life examples, so it is easy to start using this. See the documentation inside. Please give me your feedback if you use this tool. Kind regards, Andrey Fri, 13 Jun 2014 12:00:02 +0200 от gromacs.org_gmx-users-requ...@maillist.sys.kth.se: >Send gromacs.org_gmx-users mailing list submissions to >gromacs.org_gmx-users@maillist.sys.kth.se > >To subscribe or unsubscribe via the World Wide Web, visit >https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users >or, via email, send a message with subject or body 'help' to >gromacs.org_gmx-users-requ...@maillist.sys.kth.se > >You can reach the person managing the list at >gromacs.org_gmx-users-ow...@maillist.sys.kth.se > >When replying, please edit your Subject line so it is more specific >than "Re: Contents of gromacs.org_gmx-users digest..." > > >Today's Topics: > > 1. ligand topology for opls.aa (Saman Shahriyari) > > >-- > >Message: 1 >Date: Fri, 13 Jun 2014 01:32:46 -0700 (PDT) >From: Saman Shahriyari < samanshahriy...@yahoo.com > >To: Discussion list for GROMACS users < gmx-us...@gromacs.org > >Subject: [gmx-users] ligand topology for opls.aa >Message-ID: >< 1402648366.13559.yahoomail...@web163203.mail.gq1.yahoo.com > >Content-Type: text/plain; charset=iso-8859-1 > >Dear users >i wanted to know if "Acpyte" generated topologies for a ligand are compatible >with OPLS-AA.ff? i am searching for a reliable topology builder for OPLS-aa >like ATP for gromos53a6.ff so that i can avoid manual approached >like?using?"gaussian" . >?regards, >Saman > > >-- > >-- >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 122, Issue 61 >** -- -- 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] ligand topology for opls.aa
Dear users i wanted to know if "Acpyte" generated topologies for a ligand are compatible with OPLS-AA.ff? i am searching for a reliable topology builder for OPLS-aa like ATP for gromos53a6.ff so that i can avoid manual approached like using "gaussian" . regards, Saman -- 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.
