[gmx-users] Methanol geometry parameters

Fri Dec 4 14:03:43 CET 2015

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 <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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-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================