[gmx-users] Methanol geometry parameters

[Barnett, James W]

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