Gurpreet,
I didn't ask whether you used PBC, I suggested it was due to PBC.
Check the archives for "broken molecules" and such.
Tsjerk
On 7/16/07, gurpreet singh <[EMAIL PROTECTED]> wrote:
Thanks Tsjerk for you reply
i did not get your point . i think you are asking me whether i used PBC or
not , so i want to tell you that the .tpr file which i used for genion
command was created without using PBC.
but will it make any difference ?
Thanks
With Regards
Gurpreet
On 7/16/07, Tsjerk Wassenaar <[EMAIL PROTECTED] > wrote:
>
> 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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--
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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