trevor brown wrote:
Dear users,
In Gromacs 4.5.3, atom types are defined in
/share/top/oplsaa.ff/atomtypes.atp.
The corresponding bonds for diffrent atopm pairs are described as
between opls_001 and opls_965.
I have a CNT, I need C-C intereaction, which one should I choose?
I would find a similar functional group in aminoacids.rtp (i.e., aromatic ring,
presumably) and see what is used there. If you build a topology with g_x2top,
it will assign parameters for you; how accurate they are I do not know.
Second question; where can I find info about opls_XXX?
Descriptions for most are found in atomtypes.atp. Otherwise, look at how
they're used in aminoacids.rtp. Bonded type names are found in [atomtypes] in
ffnonbonded (i.e. opls_145 is CA for bonded interactions), which are then used
in ffbonded.itp.
-Justin
trevor
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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