AMBER Archive (2006)

Subject: Re: AMBER: VdW radii in the topology file

From: harianto (harianto_at_mailer.sb.fsu.edu)
Date: Mon Apr 10 2006 - 11:51:55 CDT

Hi Vlad,
I guess, you can do a simple calculation using van der Waals formula (W=
A/R12-B/R6) and taking dW/dR = 0 using L-J constants A and B listed in
your top file (%FLAG LENNARD_JONES_ACOEF and _BCOEF) you can solve for
R.
Then compare this R to ptraj output dumpq radius. I hope they are the
same, aren't they?
(But don't forget to take a look the manual (appendix part) for indexing
these coefficients.)

Goodluck,
Harianto.

On Mon, 2006-04-10 at 18:14 +0200, Vlad Cojocaru wrote:
> Dear Amber users,
>
> in ptraj "trajout [file] PDB dumpq"... dumps the VdW radii in the pdb
> file. Could somebody tell me shortly, where actually in the topology
> file are the vdw radii stored (I looked at the file formats on the Amber
> webpage and searched the archive but I couldnt really find the info)?
>
> Thanks
>
> Best
> vlad
>

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