[gmx-users] Where would I find the 45A4 GROMOS force field?

[Oliver Stueker]

Hi Marc,

Though I never came across ready-to-use files for Gromos 45A4, you can
for sure get all the parameters for carbohydrates from [1] and
transfer them into a Gromacs format (make sure to convert all the
units).

Searching briefly for the term 45A4 in [2] lets me believe, that the
parameters have been cooperated into 53A5 and 53A6, so you might want
to check that as well.

[1] Lins RD, Hunenberger PH (2005)
    A new GROMOS force field for hexopyranose-based carbohydrates.
    Journal of Computational Chemistry 26: 1400-1412.
    Available: http://dx.doi.org/10.1002/jcc.20275.
[2] Oostenbrink C, Villa A, Mark AE, Gunsteren WF van (2004)
    A biomolecular force field based on the free enthalpy of hydration
and solvation: the GROMOS force-field parameter sets 53A5 and 53A6.
    Journal of Computational Chemistry 25: 1656-76.
    Available: http://dx.doi.org/10.1002/jcc.20090.

Oliver

On Wed, Mar 28, 2012 at 07:28, Marc Gordon <marcgrdn55 at gmail.com> wrote:
> Ah well no worries. I will delve back into the gromacs and NAMD user guides
> and see what I can dig up with regards to getting these GROMOS files working
> through NAMD.
>
> Thanks again for the help you have given me.
>
> Marc
>
>
>
> On Wed, Mar 28, 2012 at 4:19 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>
>> Marc Gordon wrote:
>>>
>>> Oh awesome. Thanks so much for this.
>>>
>>> I've never worked with GROMOS or gromacs themselves. I'm going to need to
>>> look up whether or not it is possible to use these files to generate files
>>> in the gromacs format required as input for NAMD now but at least having
>>> access to the force fields puts me that much further along. I don't suppose
>>> you know offhand whether such a thing is possible?
>>>
>>
>> Sorry, but I don't.  I haven't done anything with NAMD that wasn't out of
>> the box.  That's probably a question better posed to the NAMD people.
>>
>> -Justin
>>
>>> I see they have a myriad of force fields available on ATB including the
>>> other one I am interested in 53A6.
>>>
>>> Thanks again.
>>>
>>>
>>> On Wed, Mar 28, 2012 at 2:50 PM, Justin A. Lemkul <jalemkul at vt.edu
>>> <mailto:jalemkul at vt.edu>> wrote:
>>>
>>>
>>>
>>>    Marc Gordon wrote:
>>>
>>>        Hi all
>>>
>>>        I have never posted to the mailing list before but it has proven
>>>        very helpful in the past.
>>>
>>>        I'm looking for the 45A4 force field. I've been asking Mr.
>>>        Google but so far I haven't had any luck locating it. This is I
>>>        imagine probably down to the wrong keywords or something
>>>
>>>         I want to do some work on disaccharides and I would very much
>>>        like to use this force field. I'm going to be using it thorugh
>>> NAMD.
>>>
>>>        I thought this would be the best place to ask if anyone knew of
>>>        a site where this force field was being maintained or something.
>>>
>>>
>>>    You can get the files from ATB:
>>>
>>>    http://compbio.biosci.uq.edu.__au/atb/
>>>
>>>    <http://compbio.biosci.uq.edu.au/atb/>
>>>
>>>    They are formatted for use with the GROMOS MD package, but that's
>>>    the only source of these files of which I'm aware.
>>>
>>>    -Justin
>>>