[gmx-users] VDWradii.dat

David van der Spoel spoel at xray.bmc.uu.se
Mon Aug 30 20:45:14 CEST 2010

On 2010-08-30 20.32, nishap.patel at utoronto.ca wrote:
> Hello,
> I have a question about how gromacs assigns VDW radii for ions. I
> checked the vdwradii.dat file but it does not mention any ions, so where
> do the parameters for ions come from? I got the .pqr file for sodium and
> I got the atomic radii of 1.6652A, I am not sure where that value came
> from.
> I would really appreciate some help!
> Thanks.
> -Nisha P
Did you get the pqr file from editconf? Then read editconf -h.
Check the -sig56 option.

David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se

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