AMBER Archive (2006)

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

From: Vlad Cojocaru (
Date: Mon Apr 10 2006 - 12:01:33 CDT

That's what I thought also ... Just wanted to make sure that this is the
case ...

The values printed by ptraj look very similar to the values stored in
the parm99.dat, so they should be OK ...

Maybe if I notice anything weird I'll do test calculations from the vdw
coefficients ...


harianto wrote:

>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
>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.)
>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)?
>> Best
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Dr. Vlad Cojocaru
EML Research gGmbH
Molecular and Cellular Modeling Group
Schloss-Wolfsbrunnenweg 33
69118 Heidelberg, Germany
Phone: +49-6221-533266
Fax: +49-6221-533298

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