[gmx-users] Methanol geometry parameters

[Kalev Takkis]

On 3 December 2015 at 20:05, Vitaly V. Chaban <vvchaban at 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.stern at 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-bounces at maillist.sys.kth.se [mailto:
> > gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of Daniele
> > Veclani
> > Sent: Thursday, December 03, 2015 3:31 PM
> > To: gmx-users at 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-request at 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-request at 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-request at gromacs.org.
>