[gmx-users] OPLS definition of Phenyl palmitate

[Justin Lemkul]

On 6/8/15 11:57 AM, Ebert Maximilian wrote:
> Maybe this is of interest to others so I will write what I did. I built a phenyl acetate and methyl acetate:
>
>                                   O_2
>                                     ||
>    CA - CA                 C_2
>   /              \               /     \
> CA            CA - OS        CT
>   \              /
>    CA - CA
>
>
>               O_2
>                 ||
>               C_2
>               /     \
> CT - OS        CT
>
>
> And I did a conformation search of the two molecules using QM/MM. After finding the best ideal gas solution I looked at the dihedral energy profile of CT OS C_2 O_2, CT OS C_2 CT, CA OS C_2 O_2 and CA OS C_2 CT. The pairs basically matched with the same energy minimum at the same angle. So I presume now that with a small error the approximation can be used. Of course I am not an expert as you can tell so if you have any additional thoughts please let me know.
>

The most rigorous validation is a series of single-point energy scans of 
optimized geometries at fixed values of the dihedral as it makes a full 
rotation.  This is described in the OPLS papers.  Sure, the minima may coincide, 
but are the barriers to rotation the same?  You don't know this from what you've 
done.  Likely it will be fine, but if you want to be sure, you have to actually 
be sure :)

-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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