[gmx-users] impropers in Gromacs and acepype tool

[Chetan Mahajan]

I think acepype Amber2gromacs tool has amber parameter files. but here is
no .rtp


On Thu, Mar 6, 2014 at 4:40 PM, Chetan Mahajan <chetanvm10 at gmail.com> wrote:

> Thanks, Justin. I do not have AMBER parameter set or .rtp file. I have
> just one .top file which contains topologies and parameters. Just curious:
> where to get Amber parameter set from?
>
>
> On Thu, Mar 6, 2014 at 4:25 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 3/6/14, 5:16 PM, Chetan Mahajan wrote:
>>
>>> Hi
>>>
>>> I just wanted to check the order of atoms in a improper in gromacs input
>>> file *.top. According to urea example on page 137 ( section 5.7)of manual
>>> 4.6.4, order of i,j,k,l atoms in improper always starts with central
>>> atom,
>>> whereas that in a *.top file generated with acepype lists i,j,k,l order
>>> for
>>> improper in formate ion as H O C O. Central atom at third position. Is
>>> this
>>> right or bug in the tool acepype?
>>>
>>>
>> It's right.  The example in the manual is for Gromos force fields.  You
>> should look at the actual .rtp files for the AMBER parameter set you're
>> trying to use.  Suffice it to say that different atom orders are supported,
>> because the Gromacs machinery (specifically pdb2gmx) knows how to deal with
>> lots of stuff based on bonded geometry.
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 601
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
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>
>