Gurpreet,
my system was going fine at that time but when i used the genion command to
add ions , i found that my protein was broken into parts.
what could be the reason for this ?
PBC?
While running the genion it usually asked for the group into which we want
to add the ions so i have checked with both the SOL group and OTH group
seperatly , in both the cases ions were replacing the solvent molecules. Is
their any way by which we can add ions without replacing any solvent
molecules ?
No, there's no space to put them.
Well, you could try to squeeze them in here or there manually, and
perform energy minimization...
Cheers,
Tsjerk
--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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