Thanks Dan and Jason.
Let's say one guesses the dihedrals based on the bond topology (two bonds
that share a bond). Will the dihedrals thus guessed be a subset of the
dihedrals guessed by GAFF forcefield obtained by using parmed.py (print
dihedrals).
In other words,
if one finds the unique dihedrals form the dihedrals list will this number
be equal to the dihedrals guessed on bond topology ?
Can you please clarify
Thanks
Arun
On Tue, Oct 14, 2014 at 5:13 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
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>
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Received on Tue Oct 14 2014 - 16:00:02 PDT
