Dear Stern. I apologize for the disruption.
Create pdb file is very simple. but the distances and bond angles of methanol where I find them? I do not think can I put random distances and angles? Best D.V. 2015-12-04 12:50 GMT+01:00 Barnett, James W <jbarn...@tulane.edu>: > On Fri, 2015-12-04 at 09:43 +0100, Daniele Veclani wrote: > > Dear Peter Stern. > > > > Yes, I need the starting coordination for methanol, but are there > specific > > coordinates like for spce water or tip3p water? > > > > Where can I find the files .gro or .pdb for methanol ? > > Creating a methanol pdb file should be quick with a program like Avogadro > or > maybe AmberTool's xleap. Then use "gmx solvate" to get coordinates for > water. > > > > > > > Dear Chaban > > > > Similar molecules have already been studied with this methanol. > > > > This Methanol is implemented in opls force field. > > > > I appreciate the time and effort you have spent sorting out that problem. > > > > D.V. > > > > > > 2015-12-04 8:41 GMT+01:00 Kalev Takkis <kalev.tak...@gmail.com>: > > > > > On 3 December 2015 at 20:05, Vitaly V. Chaban <vvcha...@gmail.com> > wrote: > > > > > > > You, perhaps, need to care about *compatibility* of this old > methanol and > > > > your solute molecule. > > > > > > > > > > > > > Why? General caution or do you know that there is something wrong with > it? > > > Because if I'm not mistaken, it's the same methanol distributed with > > > Gromacs. > > > > > > All the best, > > > Kalev > > > > > > > > > > > > > > > > > > > > > > > > > > > On Thu, Dec 3, 2015 at 2:08 PM, Peter Stern < > peter.st...@weizmann.ac.il> > > > > wrote: > > > > > > > > > The force field parameters are defined in ffbonded.itp and > > > > ffnonbonded.itp. > > > > > You still need starting coordinates for your molecule. > > > > > There are plenty of programs which will do this, but you can > probably > > > > find > > > > > it in some pdb entry. > > > > > But, it is also trivial to do by hand since there are only two > atoms > > > and > > > > > you know the C-O bond distance, e.g.: > > > > > HETATM 1 C MOH 1 1 0.000 0.000 1.410 1.00 1.00 > > > > > HETATM 2 O MOH 1 1 0.000 0.000 0.000 1.00 1.00 > > > > > > > > > > You should use an existing pdb or gro file as a template for the > > > correct > > > > > format. gmx pdb2gmx will add the H-atoms. > > > > > > > > > > Peter Stern > > > > > > > > > > -----Original Message----- > > > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto: > > > > > gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of > > > Daniele > > > > > Veclani > > > > > Sent: Thursday, December 03, 2015 3:31 PM > > > > > To: gmx-us...@gromacs.org > > > > > Subject: Re: [gmx-users] Methanol geometry parameters > > > > > > > > > > Thank you for your reply. > > > > > > > > > > Yes, The .itp file for methanol comes from gromacs. But but I need > the > > > > > .gro file. I need the geometric parameters like distances, angles > and > > > > > diedrals. > > > > > these parameters are not in the .itp file or I'm wrong?? > > > > > > > > > > Best regards > > > > > D.V. > > > > > -- > > > > > 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. > > > > > > > > > -- > > > > 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. > > > > > -- > James "Wes" Barnett, Ph.D. Candidate > Louisiana Board of Regents Fellow > > Chemical and Biomolecular Engineering > Tulane University > 341-B Lindy Boggs Center for Energy and Biotechnology > 6823 St. Charles Ave > New Orleans, Louisiana 70118-5674 > jbarn...@tulane.edu > -- > 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.