Thank you so much for your help, everyone. I am almost there.
Just to make sure I understand, for dihedral angles that have two sets of
parameters, the dihedral angle is calculated once, and the energy and force
is calculated using each separate pair of parameters, and the total force
and energy is summed over the two parameter set calculations?
Thank you for pointing out the "hc-c3-c -o" and "hn-n-c -o" parameters.
There was a reason I could not find them myself when looking through the
file, and maybe you can clear this up for me. The gaff.dat file lists the
following values for those dihedral parameters
hc-c3-c -o 1 0.80 0.0 -1
hc-c3-c -o 1 0.08 180.0 3
hn-n-c -o 1 2.50 180.0 -2
hn-n-c -o 1 2.0 0.0 1
However, in my prmtop file (values given in first email in this chain), the
periodicity values are given as 1 and 2 (no negative sign). What happened
to the negative sign on these periodicity values in my prmtop file?
Regards,
Conor Parks
B.S.E in Chemical Engineering, University of Michigan, 2012
PhD candidate in Chemical Engineering, Purdue University
On Tue, May 3, 2016 at 11:05 AM, David A Case <david.case.rutgers.edu>
wrote:
> On Mon, May 02, 2016, conor parks wrote:
> >
> > ....by dihedral pairs, I mean the set of four atoms that make up a
> > dihedral angle. Perhaps I should have chosen a better term than pair! As
> > you suggested, I looked in to parmed. Thank you for showing me this, as I
> > was not previously aware of this utility. It seems the issue is that when
> > antechamber generated the prmtop file, it lists two sets of parameters
> for
> > one dihedral angle. Specifcially, this is what I find.
> >
> > printDihedrals .6
> > ... (list of all other parameters)
> > 6 O2 ( o) 5 C7 ( c) 7 N1 ( n) 8
> > H6 ( hn) 2.0000 1.0000 0.0000 1.2000 2.0000
> > M 6 O2 ( o) 5 C7 ( c) 7 N1 ( n) 8
> H6
> > ( hn) 2.5000 2.0000 180.0001 1.2000 2.0000
>
> This is expected: many torsional profiles are represented by multiple terms
> with different periodicity. In this case, terms with periodicities of 1
> and 2
> are added together to get the total torsional term.
> >
> > printDihedrals .1
> > ....(list of all other parameters)
> > M 4 H9 ( hc) 1 C8 ( c3) 5 C7 ( c) 6
> > O2 ( o) 0.0800 3.0000 180.0001 1.2000 2.0000
> > 4 H9 ( hc) 1 C8 ( c3) 5 C7 ( c)
> > 7 N1 ( n) 0.0000 2.0000 180.0001 1.2000 2.0000
> >
> > Could someone tell me what that M means?
>
> This torsion is part of a "multiple" torsion set (Jason can correct me if
> this is wrong.)
>
> > Also, it is not clear to me where
> > the M parameters come from. I looked thoroughly through the gaff.dat
> file,
> > and count not find these M-sets of parameters for any IDIVP. The non-M
> > parameters come from the X -c -c3-X and X -c -n -X dihedral parameter
> > values. Could someone explain to me what is happening?
>
> There is a specific "hc-c3-c -o " set of torsions in gaff.dat, as well
> as an "hn-n -c -o " set of torsion parameters. These are where the
> torsions
> you cite above come from.
>
> ...dac
>
>
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Received on Tue May 03 2016 - 09:00:03 PDT
