[gmx-users] Parameter conversion from GAFF to Gromacs

Rohit Farmer rohit.farmer at gmail.com
Thu Oct 16 19:24:35 CEST 2014

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.



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