[gmx-developers] importing amber parameters to gromacs format?

Justin Lemkul jalemkul at vt.edu
Tue Aug 8 03:12:05 CEST 2017

On 8/7/17 2:47 PM, Ming wrote:
>   Hi gromacs team,
> I am trying to simulate a protein ligand complex using gromacs, where I have two 
> manganese ions bound with the ligand. I searched the gromacs force field and 
> there was no parameter data for Mn. After some research online I found the 
> following Amber link that has Mn parameters. Some online constructions says 
> ffamber ports can do the work, but there were no more detailed instructions. I 
> don't have much experiences converting amber parameters to files that gromacs 
> can recognize, so I want to see if anyone here can help me on this by giving me 
> some more detailed instructions?

Please ask general usage questions on the gmx-users mailing list.  I am CCing 
this message there and ask that any further questions be posted there. 
gmx-developers is for discussion of code and development.

This is just a unit/format conversion issue.  The AMBER manual will (should) 
describe the format of its force field files, and the GROMACS manual describes 
its required format.  Beyond syntax of the files, it's just a matter of 
converting kcal -> kJ and A -> nm, and maybe computing LJ parameters if the 
AMBER specification differs from that of GROMACS (sigma and epsilon).



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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