On 9/9/12 7:53 AM, Matthias Ernst wrote:
Hi,
I just encountered (another) strange thing with genion.
I wanted to neutralized a system by adding Mg-Ions (charge in ions.itp: 2,
forcefield amber99sb), so I expected half of the system charge (-52) to be added
as ions. BUT it added the same amount, i.e. 52 Mg ions instead of 26 which would
be needed for neutralization. The same holds for Zn or Ca ions, which also are
divalent in ions.itp
Charge is not read from ions.itp, it is taken from the command line. The value
of -pq is 1, so if you're adding divalent metals, set it to 2.
Could it be that the routines of genion to determine the number of ions are not
working properly? I mean, the -neutral option also does work only if the -conc
flag is also there and provides a value > 0.0 (which in fact is not what I want
when I just want do neutralize my system by adding ions...)
This has been an issue for a long time. I suppose no one has ever filed a
redmine issue for it, so please do. Otherwise, it won't get fixed.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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