[gmx-users] Methanol geometry parameters

[Daniele Veclani]

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 ?


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.takkis at gmail.com>:

> 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.
> > > --
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