[gmx-users] impropers in Gromacs and acepype tool

[Chetan Mahajan]

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
>
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> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
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>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
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