Hi all,
Thank you very much for your responses.
Andrew, here is my ac.frcmod:
MASS
BOND
ANGLE
DIHE
IMPROPER
c3-n -c -o 10.5 180.0 2.0 General
improper torsional angle (2 general atom types)
c -ca-n -hn 1.1 180.0 2.0 General improper
torsional angle (2 general atom types)
ca-ca-ca-n 1.1 180.0 2.0 Using default
value
ca-ca-ca-ha 1.1 180.0 2.0 General improper
torsional angle (2 general atom types)
ca-ca-ca-oh 1.1 180.0 2.0 Using default
value
NONBON
There appears to be no missing dihedral parameters.
Dac, 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
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? 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?
Regards,
Conor Parks
B.S.E in Chemical Engineering, University of Michigan, 2012
PhD candidate in Chemical Engineering, Purdue University
On Sun, May 1, 2016 at 8:42 AM, David A Case <david.case.rutgers.edu> wrote:
> On Sun, May 01, 2016, conor parks wrote:
> >
> > 1) broadly speaking, is there anyway to know the list of dihedral pairs
> > being used.
>
> I'm not sure what you mean by the phrase "diehdral pairs". But the
> printDihedrals command in parmed will format the dihedrals in a nice way,
> and that may help you understand what is going on.
>
> See also the other print* commands in parmed.
>
> ...hope this helps...dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon May 02 2016 - 09:30:03 PDT
