[gmx-users] (no subject)

[Justin Lemkul]

On 3/1/15 10:32 AM, Tushar Ranjan Moharana wrote:
> Hi everyone,
> I want to simulate lid opening of lipase in presence of micelles of
> triglyceride having both saturated and *cis* polyunsaturated fatty acids
> (separately). When I did it using GROMOS 54a7 I didn't get appropriate
> result. It seems as if the forcefield doesn't considered unsaturation. When
> I use CHARM36 everything was fine till energy minimization but when I did
> nVT or nPT simulation the unit cell which was a cube becomes a rectangular
> slab and the worse thing was all the triglyceride molecule goes out of the
> unit cell. When I try OPLSAA I am getting "No default Proper Dih. types"
> also the total charge is non integer.I use topolbuild 1.3 to create .itp
> file of my triglyceride. Please let me know Which forcefield I should use
> and how shall I make .itp (or topology) file for triglyceride containing
> *cis* polyunsaturated fatty acid (for example EPA or DHA) and any other
> modification I shall do to any file of that forcefield.
>

The CHARMM36 force field is likely the best here.  The symptoms you describe 
above likely stem from incorrect construction of the system or simple 
periodicity effects.

-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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