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

[Justin Lemkul]

On 1/19/16 4:36 AM, carlos.navarro87 at gmail.com wrote:
> 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.

The link I provided points directly to:

"CHARMM36 Files for GROMACS

CHARMM36 force field in GROMACS format, including CGenFF version 3.0.1. Updated 
July 6, 2015.

charmm36-jun2015.ff.tgz"

That's the full CHARMM36 force field, which contains all the parameters you 
need.  If there's something you can't find, please say exactly what it is that 
you need; referencing "parameters" is ambiguous.  The .rtp file has things like 
atom types and charges, ffbonded.itp and ffnonbonded.itp have bonded and 
nonbonded interaction parameters, etc.

-Justin

> 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
>
> ==================================================
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
>

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

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

==================================================