AMBER Archive (2005)

Subject: RE: AMBER: TI - frcmod file

From: Rhoad, Jonathan S. (rhoadj_at_missouri.edu)
Date: Wed Jul 13 2005 - 16:03:17 CDT

Ilyas Yildirim wrote:

>CT-CT-C -N 1 0.100 0.0 -4.
phi,psi,parm94
>CT-CT-C -N 1 0.07 0.0 2.
phi,psi,parm94
>
>Then, after the second parameter load (frcmod.03), what will be the
torsional parameters of CT-CT-C -N? I thought that the last column
(above, it is -4 and 2) is defining if there are multiple torsional
parameters for a particular torsion angle. So, if we wanted to change
them, we should have used the following format: (at least that's what I
have understood)

>CT-CT-C -N 1 XXXXX XXX -4.
>CT-CT-C -N 1 XXXXX XXX 2.

>But in frcmod.03 file, the torsional parameters for CT-CT-C -N are
defined
>as following:

>CT-CT-C -N 1 0.0560 0.00 -3.
>CT-CT-C -N 1 0.0657 180.00 -2.
>CT-CT-C -N 1 0.7784 180.00 1.

>I am thinking that these extra three torsional parameters for CT-CT-C
-N
are going to be added on the CT-CT-C -N parameter list (because their PN
number are different; -4,2,-3,-2,1). If I am wrong, please correct me.
If
it overwrites the parameter list, how does it do it? Just deletes the
whole CT-CT-C -N torsional parameter list previously defined, and then
adds the new parameter list?

As I understand it, when leap write the parameters, it reads through the
parameters that were loaded _backwards_, and the first parameter that it
comes across for a certain dihedral (or angle or bond or improper
dihedral etc. is used) and the rest are ignored. Therefore whichever
force field or frcmod that was loaded _last_ is used in the
parameter/topology file. So in this case if the upper dihedral were
loaded first, only the second would be used.

Someone more expert can correct me if I am wrong.

Jonathan Rhoad
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