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 _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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