AMBER Archive (2008)

Subject: RE: AMBER: to understand how frcmod.ff99SB works

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Thu Aug 28 2008 - 16:58:03 CDT

> Amber allows multiple dihedrals but only if the periodicity is different for each dihedral. So in the case below the -4 and -3 periodicity entries are added as additional dihedrals while the -2 and 1 entries in frcmod.ff99SB should overwrite the existing two entries from parm99.dat.
>
> Loading any additional parameters with the same atom types and matching periodicities will overwrite existing entries already loaded that match that atom type set and periodicity. Hence why FF99SB has
>
> C -N -CT-C 1 0.00 0.0 1.
>
> This is equivalent of deleting the original 0.8 barrier height dihedral from parm99.dat.
>
> I hope this helps,
>
> Ross

Ross, I thought the way frcmod works is as follows: If you define any
dihedrals in the frcmod file, it will first remove all the entries from
the previously defined force field and add the new entries to leap. Let's
say that my xleap commands are like this:

---- xleap.in -----
source leaprc.rna.ff99
loadamberparams frcmod
-------------------

and let's say my frcmod file is as follows:

----- frcmod -----
Modified dihedral parameters
MASS

BOND

ANGL

DIHE
OS-CT-N*-CK 1 5.00 000.0 2. parm98,
IMPR

NONB
------------------

What this will do is, it will remove any entries defined for OS-CT-N*-CK
and only add this particular dihedral parameter. This means that in the
prmtop file, there will be only 1 parameter set defined for this
particular dihedral. In the amber99.dat file, there are 2 sets defined for
this particular dihedral (2 periodicities).

OS-CT-N*-CK 1 0.00 000.0 -2. parm98,
OS-CT-N*-CK 1 2.50 0.0 1. parm98,

So, having the above frcmod file will remove the above entries and add
parameters for the periodicity n=2 only. I just double checked this
using rdparm. So, I dont think that there is any reason to define zero
parameters for the unwanted entries (except that if someone is doing TI
calculation and have this particular entry nonzero). 

-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
  = Department of Physics        -                              =
  = University of Rochester      -                              =
  = 585-275-6766 (office)        - 585-267-5644 (home)          =
  = http://www.pas.rochester.edu/~yildirim/                     =
  ---------------------------------------------------------------

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