You, perhaps, need to care about *compatibility* of this old methanol and your solute molecule.
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.