[gmx-users] Methanol geometry parameters

[Daniele Veclani]

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 <jbarnet4 at 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.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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> --
> 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
> jbarnet4 at tulane.edu
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