AMBER Archive (2006)

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

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Thu Aug 03 2006 - 10:33:34 CDT

have you read the information on the Amber web page about the format of this
file? Let us know if this doesn't answer the questions.
http://amber.scripps.edu/formats.html#parm.dat

Lwin, ThuZar wrote:

> 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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