From: Ross Walker <>
Date: Fri, 17 Jul 2009 04:40:11 +0100

Hi Bill,

> If the author didn't specify the IDIVF factor in dihedral parameter in
> his paper, so should I assume it equal to one?

Yes. Note IDIVF is generally only used for wild cards. E.g X-CA-CA-X. When
you explicitly define all 4 atoms it should generally be set to 1.

> Also, in Amber file format, under dihedral section, it states that:
> "The negative value of pn is used only for identifying the existence of
> the next term and only the absolute value of PN is kept." Sorry, what
> does "absolute value is kept" mean?

It means: ABS(-X) = X. I.e. just the value is kept, the - sign is discarded.
So essentially this means if, for a given set of 4 atoms you have one
dihedral then the last value should be +ve. If you have 2 or more then the
first N-1 dihedrals for this specific torsion should have -ve PN values and
the last one should have a +ve value.

> For example, in parm99
> HC-CT-CM-CM   1    0.38        180.0            -3.         Junmei et
> al, 1999
> HC-CT-CM-CM   1    1.15          0.0             1.         Junmei et
> al, 1999
> what is the PN here for this dihedral bond?

So this says for the dihedral HC-CT-CM-CM there are 2 torsion terms in use.
A 3 fold one and a 1 fold one. In this case the last entry has a +ve value
for PN (1 here) while the earlier one (-3) has a -ve value.

All the best

|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
| | PGP Key available on request |

Note: Electronic Mail is not secure, has no guarantee of delivery, may not
be read every day, and should not be used for urgent or sensitive issues.

AMBER mailing list
Received on Fri Jul 17 2009 - 01:08:28 PDT
Custom Search