[gmx-users] Methanol geometry parameters

[Peter Stern]

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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