[gmx-users] problem with genion
tsjerkw at gmail.com
Mon Jul 16 09:27:57 CEST 2007
> 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 ?
> 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...
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
3584 CH Utrecht
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