[gmx-users] Alkane parameters for charm forcefield on gromacs

[Justin Lemkul]

On 1/18/16 1:39 PM, carlos.navarro87 at gmail.com wrote:
> Dear gmx users,
> I’m trying to construct CG parameters for an specific molecule, let’s call it 'A'.
> To do that, I first need to run a MD simulation of ‘A’ solvated by a polar (water) and non polar (alkane) solvent. (I’m looking for octane and hexadecane, but any alkane with a ‘long’ chain should work).
> Since the parameters for ‘A' I got them from http://www.swissparam.ch/, I need also the parameters of the alkane solvent from charmm to run the MD.
> Sadly, I haven’t found anything (probably I haven’t search in the right place).
> Could someone help me to find such parameters?

We provide several short alkanes in our CHARMM36 distribution.

http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs

PRPA = propane, BUTA = butane, IBUT = isobutane, PENT = pentane, etc.

As you can see, extension of alkane chains is trivial by simply adding methylene 
units that all have the same parameters.

-Justin

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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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