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.
Neither can anyone else unless you provide the command you gave that produced
this result as well as the force field you're using. Presumably you generated
your .pqr file with editconf? In that case, have a look at the code starting
around line 587 (in the 4.0.7 source) for the decision structure that dictates
how the value of "vdw" is assigned.
-Justin
I would really appreciate some help!
Thanks.
-Nisha P
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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