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/ -
---------------------------------------------------------------
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Mon Jan 10 2005 - 22:53:00 PST
