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

[carlos.navarro87 at gmail.com]

Hi Justin,
Thanks for your kind reply.
I have been looking in all files/links for the parameters of short alkanes without luck, would you be so kind to tell me which specific link should I download?
Sorry for all the troubles.
Best,
Carlos

-- 

Carlos Navarro Retamal
Ingeniero en Bioinformática
Ph. D (c) en Ciencias Aplicadas.
Centro de Bioinformática y Simulación Molecular
Universidad de Talca
Av. Lircay S/N, Talca, Chile 
T: (+56) 712201 798
E: carlos.navarro87 at gmail.com o cnavarro at utalca.cl

On January 18, 2016 at 3:45:15 PM, Justin Lemkul (jalemkul at vt.edu) wrote:



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

--  
==================================================

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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