I think that this number are polarizabilities. This ones are adding in
frcmod file next to the mass and don´t work if you do not run sander with
the keyword IPOL.
G.
At 05:10 p.m. 10/01/2005, you wrote:
>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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Received on Tue Jan 11 2005 - 10:53:01 PST
