AMBER Archive (2005)

Subject: Re: AMBER: .dat and frcmod files

From: Anthony Fejes (fejes_at_zymeworks.com)
Date: Mon Jan 10 2005 - 16:47:12 CST

Hi Ilyas,

There is some excellent documentation available on the web. A quick
google search pulled up:

http://amber.scripps.edu/formats.html

If you scroll down towards the bottom, you'll find a header that reads:

"Force field parameter file specification"

This section should answer a lot of your questions.

Anthony

Ilyas Yildirim 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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