AMBER Archive (2006)

Subject: AMBER: Need to know meaning of numbers in parm99.dat file to be able to write frcmod file for dummy atoms

From: Lwin, ThuZar (ThuZar.Lwin_at_stjude.org)
Date: Thu Aug 03 2006 - 10:14:28 CDT

Hi,

    I am trying to understand clearly what those values in parm99.dat
file stand for. While I can guess some for sure, I can not figure out
for others.

Here are my questions:

 

1. For each atom, there are two columns:

    CA 12.01 0.360 : what does 0.360 mean? I also notice that
some atoms have two columns and some only have the mass.

 

2. For dihedral, there are four columns:

    CT-CT-N -C 1 0.50 180.0 -4. : which
ones correspond to Vn, n, psi and gamma as described on pg 89 of amber8
manual AND what is the meaning of

 
"the negative sign" in front of number 4.

3. For the non bonded parameters for dummy atom as described in the
tutorial of TI by Dr. Case:

    DH 1.0000 0.000

    DC 1.0000 0.000 : what
do those numbers mean and stands for?

 

Thank you very much,

tz

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