Date: Wed, 9 Nov 2011 14:20:30 -0800 (PST)
Dr. Case, Thanks for the suggestion. Yes it fixes the solvateOct problem. The reimaged WAT layers look kind of weird (picture is attached). I hope that equilibration step would fix this. Senthil P.S: I believe that Jan's contribution was relevant to this discussion/thread OK...this is probably my fault, although both you and Senthil Natesan are writing on the same thread, and maybe I got things mixed up. But I suspect that I am not the only person that is now confused. If you are happy with the "combine approach" and everything works as expected without any bugs, that is great. If you have other questions/problems, please start a new thread on the mailing list (that is, don't use the "reply" command, but compose a new mail with a new subject.) The problem I *thought* was occuring was that solvateOct seemed not to be working correctly when the "combine approach" was used. For this problem, I ask that the following ptraj actions be taken: input the prmtop and inpcrd files you have center the protein + ligand image familiar the water residues use trajout to save a new restart file Then look at that restart file: is the protein+ligand now in the center of the box? ....dac _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amber
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