On Wed, 2014-10-08 at 10:09 -0400, Arun Srikanth wrote:
> Hello Amber users.
>
> I am using LAMMPS for my simulation with GAFF forcefield. I would like to
> assign dihedral types correctly in my simulation.
>
> I used parmchk2 with -a option to get all the parameters for my molecule. I
> would like to know what the numbers signify with respect to the dihedral
> expression in GAFF vn, n, phi, gamma. The following is from parmchk-2
>
> c3-c3-n3-c3 1 0.300 0.000 -3.000
> c3-c3-n3-c3 1 0.480 180.000 2.000
> c3-c3-n3-hn 1 0.300 0.000 3.000
> c3-n3-c3-h1 1 0.300 0.000 3.000
> c3-c3-c3-c3 1 0.180 0.000 -3.000
> c3-c3-c3-c3 1 0.250 180.000 -2.000
>
> It would extremely helpful to know which column signifies vn, n and gamma
>
> I am not sure about this
>
> First col=n
> second =Vn
> third=phi
> fourth is gamma ??(the phase lag)
I'm not sure what you mean by "phase lag". The fourth column is the
periodicity. A negative sign means that the torsion parameter includes
the next term.
You can find more information on Amber file formats from
http://ambermd.org/formats.html
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Oct 08 2014 - 07:30:03 PDT
