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
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
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http://mackerell.umaryland.edu/~jalemkul
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