[gmx-users] Methanol geometry parameters

Fri Dec 4 14:01:09 CET 2015

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.

Sent from my iPhone

> On 4 Dec 2015, at 2:39 PM, Daniele Veclani <danieleveclani at 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 <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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