[gmx-users] impropers in Gromacs and acepype tool

[Justin Lemkul]

On 3/6/14, 5:42 PM, Chetan Mahajan wrote:
> I think acepype Amber2gromacs tool has amber parameter files. but here is
> no .rtp
>

What I am referring to are standard Gromacs force field files that come with the 
Gromacs software.  If you intend to use Gromacs for your simulations, you would 
do well to read the manual about what these files are and how they are used. 
Understanding their contents would have cleared up several of your questions 
already.

-Justin

>
> 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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>>
>>

-- 
==================================================

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

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