[gmx-users] ion parameters in amber99sb

[Justin Lemkul]

On 10/4/16 10:16 AM, Irem Altan wrote:
> Is this where I should be looking: http://repo.or.cz/gromacs.git/history/HEAD:/share/top/amber99sb.ff/ffnonbonded.itp
> If so, there doesn’t seem to be much information there.
>

You'll probably have to consult the AMBER documentation and force field files. 
 From Eric Sorin's lab (who did the original ffamber ports):

http://ffamber.cnsm.csulb.edu/ffamber.php

"(7)	(!) Using AMBER ions: Our AMBER ports include common ion definitions, which 
are listed in the ffamber*.rtp files (just below the TIP water models). This 
allows the AMBER ports to be used without modification or use of the GROMACS 
ions.itp file. At the moment these include Cl- , IB+, Na+, K+ , Rb+, Cs+, Li+ , 
Ca2+, Mg2+, Zn2+, Sr2+, and Ba2+."

You'll need to use the AMBER documentation to figure out what "common ion 
definitions" means, or at least compare the nonbonded parameters in 
ffnonbonded.itp to identify them.

-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

==================================================