AMBER Archive (2005)

Subject: AMBER: .dat and frcmod files

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Mon Jan 10 2005 - 16:10:36 CST


Dear All,

In the parm99.dat file, there are parameter informations stored for
different types of atoms. For instance the first line, it is given as
follows:

C 12.01 0.616 ! sp2 C carbonyl group

This is a carbon atom, C (or type lets say), which has a mass of 12.01. I
do not know what 0.616 corresponds to. My question is, what kind of
parameter informations are stored in the .dat files? For instance, if I
want to create an .frcmod file for a specific type I am creating, what
kind of informations should I put. And how? In some of the other lines of
this .dat file, there are informations such as this:

C H HO N NA NB NC N2 NT N2 N3 N* O OH OS P O2

or

OW-HW 553.0 0.9572 ! TIP3P water
HW-HW 553.0 1.5136 TIP3P water

or

HW-OW-HW 100. 104.52 TIP3P water
HW-HW-OW 0. 127.74 (found in crystallographic water with 3
bonds)

or

X -X -C -O 10.5 180. 2.
JCC,7,(1986),230
X -O2-C -O2 10.5 180. 2.
JCC,7,(1986),230

or

MOD4 RE
  H 0.6000 0.0157 !Ferguson base pair geom.
  HO 0.0000 0.0000 OPLS Jorgensen,
JACS,110,(1988),1657
  HS 0.6000 0.0157 W. Cornell CH3SH --> CH3OH FEP

or

Polarizabilities:
Mg2+ 0.120
F- 0.9743

additional parameters of LP

H1-CT-NT-LP 1 0.000 0.000 3.000
CT-CT-NT-LP 1 0.000 0.000 3.000

etc.

I would like to know what these data mean, like the meaning of the numbers
given, and how to create an frcmod file for a specific type we are
creating, etc. If you can direct me any reference/website, I will be
greatfull. Thanks in advance.

Best,

 --
  Ilyas Yildirim
  ---------------------------------------------------------------
  - Department of Chemisty - -
  - University of Rochester - -
  - Hutchison Hall, # B10 - -
  - Rochester, NY 14627-0216 - Ph.:(585) 275 67 66 (Office) -
  - http://www.pas.rochester.edu/~yildirim/ -
  ---------------------------------------------------------------

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