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 - 08:30:03 PDT
