On 2010-08-30 20.32, nishap.pa...@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.
sp...@xray.bmc.uu.se http://folding.bmc.uu.se
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