[gmx-users] Protein-ligand opls ff

[Chetan Puri]

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
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
>
> ==================================================
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> Gromacs Users mailing list
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