Hi,
On Mon, Oct 13, 2014 at 1:12 AM, Arun Srikanth <askforarun.gmail.com> wrote:
> 1. Is the scaling factor for the AMBER force field same for GAFF (1/2 and
> 1/1.2 for vdw and eel respectively )for all 1-4 interactions (whether they
> define a dihedral or not)
Yes; the 1-4 scaling factors for GAFF are the same as those used for
protein FFs in Amber.
> 2. The second question is regarding my earlier post. I had raised a
> question on what the "M" indicates when one uses parmed.py to print
> dihedrals. The reply from Dr. Jason was
>
> Should one specfically exclude the the eel and vdw when M is printed for
> those dihedrals ?
When calculating the 1-4 terms you should only include "normal"
dihedrals, i.e. do not include multi-term (M, referred to as 'E' for
'end' in cpptraj/rdparm), improper 'I', or both 'B' dihedrals.
Impropers aren't really 1-4 pairs, and as Jason stated before if you
include the 'end' dihedrals then you are over-counting certain 1-4
pairs.
-Dan
>
> Can someone please clarify.
>
> Thanks
> Arun
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--
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Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
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Received on Tue Oct 14 2014 - 14:30:03 PDT
