[gmx-users] Protein-ligand opls ff

[Justin Lemkul]

On 2/24/17 1:12 AM, Chetan Puri wrote:
> I want to use Desmond out.cms file for gromacs, as I want to compare MD
> output from Desmond and gromacs .
> Since Desmond uses OPLS, I will also be needing OPLS in Gromacs

If you previously ran the simulation in another program, presumably you have all 
the parameters you need, solving your problem.  You just need to put the 
topological information in the right format (see Chapter 5 of the GROMACS 
manual).  You'll have to find a way to extract useful information from a .cms 
file (whatever that contains) or from the source files from which it was generated.

-Justin

> On 24 Feb 2017 12:11 am, "Justin Lemkul" <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 2/23/17 10:53 AM, Chetan Puri wrote:
>>
>>> I have few questions
>>> 1) I tried topolgen script but it doesn't assign proper atoms, so if I
>>> change the atom type, what will happen to bonds and angles
>>>
>>>
>> Is there a reason you want to use OPLS/AA?  Most other force fields have
>> widely used ATP parameters built into the force field, requiring no work on
>> your part. Some ATP parameters may be published as part of OPLS/AA, but I'm
>> not sure how good they are.  As to benzoic acid, that's a straightforward
>> molecule to parametrize by analogy.  All force fields have aromatic rings
>> and acid groups. You just need to put them together.
>>
>> 2) can we use Desmond output for gromacs directly
>>>
>>
>> Define "output" and its format.  To do anything with GROMACS, though, you
>> need a GROMACS-formatted topology, which is usually the hardest part.
>> GROMACS will read in many different coordinate formats, so there's no real
>> barrier there.
>>
>> -Justin
>>
>> On 22 Feb 2017 7:29 am, "Chetan Puri" <chetanpuris at gmail.com> wrote:
>>>
>>> I am from Organic chemistry background and I don't know much about
>>>> inorganic chemistry calculations.
>>>>
>>>> So I would request you if you could guide me , how to generate a topology
>>>> file for a small molecule.  e.g. ATP or benzoic acid for OPLS ff
>>>> On 21 Feb 2017 11:34 pm, "Justin Lemkul" <jalemkul at vt.edu> wrote:
>>>>
>>>>
>>>>
>>>> On 2/21/17 12:56 PM, Jonathan Saboury wrote:
>>>>
>>>> I'm very inexperienced, so probably shouldn't be giving advice, but I
>>>>> think
>>>>> the below is correct :)
>>>>>
>>>>> Justin Lemkul has made many tutorials that have been invaluable to me.
>>>>> Below is his tutorial on how to prepare such a system using the GROMOS96
>>>>> 43A1 force field. (This can be changed to OPLS-AA/L all-atom force field
>>>>> during the "gmx pdb2gmx -f 3HTB_clean.pdb -o 3HTB_processed.gro -water
>>>>> spc"
>>>>> step.)
>>>>>
>>>>>
>>>>> OPLS/AA + SPC is not a combination that I'm aware of as having been
>>>> tested. TIP3P or SPC/E should be used with OPLS/AA based on the original
>>>> parametrization (TIP3P) and a published systematic analysis of hydration
>>>> free energies of amino acid analogues (SPC/E), respectively.
>>>>
>>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx
>>>>
>>>>> -tutorials/complex/index.html
>>>>>
>>>>>
>>>>> In general, the protocol is the same, but beware the details.
>>>>
>>>>
>>>> Since you already have your ligand .top file you just need to copy and
>>>>
>>>>> paste the ligand.itp line from that .top to your new one.
>>>>>
>>>>>
>>>>> I believe the question was in reference to how one would produce the
>>>> topology file for the ligand.  If one already has it, of course
>>>> proceeding
>>>> is trivial. Perhaps the OP can clarify the nature of the difficulty.
>>>> There
>>>> are a number of tools and scripts for creating OPLS/AA ligand topologies
>>>> (just a Google search away!), but of course there is no substitute for
>>>> careful examination of the literature, which for OPLS/AA is going to
>>>> require some understanding of QM calculations in the event that
>>>> corresponding or analogous parameters are not already available.
>>>>
>>>> -Justin
>>>>
>>>> --
>>>> ==================================================
>>>>
>>>> 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
>>>>
>>>> ==================================================
>>>>
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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
>>
>> ==================================================
>> --
>> Gromacs Users mailing list
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>> * Please search the archive at http://www.gromacs.org/Support
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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

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