[gmx-users] CNT

Justin A. Lemkul jalemkul at vt.edu
Sat Jan 15 23:02:20 CET 2011

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.


> trevor


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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