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 <mark.j.abra...@gmail.com> 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 <jalem...@vt.edu> 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 Please this GitHub link is totally outdated and not linked in any 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 <s.shek...@gmail.com> > 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 <jalem...@vt.edu> > > 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 <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://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 <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. > -- > 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 <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? 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