[gmx-users] Protein-ligand opls ff

[Chetan Puri]

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

2) can we use Desmond output for gromacs directly
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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