[gmx-users] Parameter conversion from GAFF to Gromacs

[Justin Lemkul]

On 10/16/14 1:24 PM, Rohit Farmer wrote:
> Hi All,
>
> I have recently converted the whole of GAFF parameters database to Gromacs
> format to use with the AMBER 99SB ILDN forcefield. My intention was to
> simulate a number of ligands which I covalently bound to a residue in the
> protein. So if I bind something to a residue then I am effectively adding a
> new residue in the system. Therefore I though I might convert the GAFF
> database and integrate it into Gromacs databases. I did it successfully and
> it seems everything is working fine as well.
>
> But I did have query regarding the conversion formulae I used for the bond
> length and angle constants. Bond anlge constant in GAFF is in kcal/mol/rad2
> where as in Gromacs its in kJ/mol/rad2 so the conversion formula which I
> used was (gaff value * 4.184 * 2). I actually took this conversion formulae
> from amb2gmx.pl script which many people use. I understand that we need to
> multiply gaff value with 4.184 to convert Kcal to KJ but I did not
> understand why we need to multiple the whole thing by 2. Can somebody
> please help me with this unit conversion stuff. I might be just stupid in
> not knowing simple chemistry.
>

It's a matter of convention.  Some programs use k/2 in their parameter files, 
other programs use k and then divide by 2 when calculating forces.  In Gromacs 
topologies and force field files, specify k directly.

-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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