On 12/4/15 8:01 AM, Peter Stern wrote:
And there are no bond angles in methanol aside from the ones involving hydrogen
atoms and these are added automatically by pdb2gmx.
As I already wrote, and Justin pointed out, the only geometric information that
you need is the C-O bond length, which is given in the force field Ito file.
For water there are no coordinates, just the single O atom. Again, H's are
added.
A quick note, though: H are only added if suitable entries are found in the
force field .hdb file. pdb2gmx does a lot of tricks, but it's not necessarily
magic.
-Justin
Sent from my iPhone
On 4 Dec 2015, at 2:39 PM, Daniele Veclani <danielevecl...@gmail.com> wrote:
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 <jbarn...@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.tak...@gmail.com>:
On 3 December 2015 at 20:05, Vitaly V. Chaban <vvcha...@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.st...@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-boun...@maillist.sys.kth.se [mailto:
gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of
Daniele
Veclani
Sent: Thursday, December 03, 2015 3:31 PM
To: gmx-us...@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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