On Mon, Oct 13, 2014 at 3:12 AM, Arun Srikanth <askforarun.gmail.com> wrote:
> Hello amber users. I am using the GAFF force field in my simulations. I
> have a couple of questions
>
> 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 are the same.
> 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
>
>
> A "M" indicates that
> "the end-group interactions are neglected (i.e., the 1-4 vdW and 1-4
> electrostatic interactions are not calculated for that torsion). This
> occurs in rings with 6 atoms or fewer and for all but one term of a
> multi-term dihedral (I originally chose "M" to indicate "multiterm", but
> it also applies to ring torsions that have only 1 term but whose
> end-groups are excluded by virtue of being 1-3 or 1-4 partners of a
> different group)."
>
> I have benzene ring in my system
>
> As such the GAFF force includes the vdw and eel (scaled) for all 1-4
> interactions.
>
> Should one specfically exclude the the eel and vdw when M is printed for
> those dihedrals ?
>
Yes, but only for atoms 1 and 4 of that ONE particular torsion term.
The rule of thumb is: compute the scaled nonbonded interactions (using
the scaling factors you mentioned above) for atoms 1 and 4 of every torsion
that does not have "M" or "I" printed next to it in the ParmEd output.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Oct 14 2014 - 14:30:02 PDT
