Re: [AMBER] How to apply extra dihedrals

From: Jason Swails <>
Date: Tue, 16 Mar 2010 23:29:20 -0400


On Tue, Mar 16, 2010 at 11:19 AM, Lekpa Duukori <> wrote:
> Hi Everyone,
> I have a question about how extra dihedrals are applied.
> My study involves  a situation where I need to apply an extra N-CT-CT-AO
> dihedral ( AO being a new atom type ).
> I make a frcmod file as follows
> N -CT-CT-AO   1    0.156        0.0             -3.
> N -CT-CT-AO   1    2.839        0.0              2

This will override the wild-card definitions in the parm file. This
is because this parameter was defined last. If, for instance, you did
not use a -3 for the first line, then the second line would overwrite
the first (because a positive value in the last column tells leap to
terminate the series). However, for those dihedrals that the
wild-cards match that your definition above does not, those will still
take the values defined by the wild-card.

This is the same as re-defining atomic parameters, such as the vdw
parameters for a pre-defined atom type. In fact, I'm pretty sure that
frcmod.ff99SB operates on this presumption (namely that because the
ff99SB dihedrals are defined after parm99.dat is sourced, those
parameters overwrite the ones present in parm99.dat).

I'm 99% sure this is how it works, though I have not written the code
(since the code has been in the field far longer than I have :) ).

Good luck!

> with the first line being the original generic X-CT-CT-X included in the
> AMBER .dat files.
> My question is: does AMBER still apply this X-CT-CT-X term to my dihedral as
> that would be double counting?
> Another option would be to edit the parmset in xleap and add only the new V2
> dihedral but I am not sure if it also applies the generic one in this case
> as in the parmset X-CT-CT-X does not have the negation on PN.
> Thanks.
> Lekpa
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Tue Mar 16 2010 - 21:00:02 PDT
Custom Search