[gmx-users] Parameter conversion from GAFF to Gromacs

[Rohit Farmer]

Thanks Justin

On Thu, Oct 16, 2014 at 6:29 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> --
> ==================================================
>
> 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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