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
--
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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
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