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-- Jason M. Swails Quantum Theory Project, University of Florida Ph.D. Candidate 352-392-4032 On Apr 28, 2011, at 12:10 PM, Oliver Kuhn <oak.amber.googlemail.com> wrote: > Ok. I'm sure I get along somehow without the perl version since I just have > to modify the input for the minimization step. > > Cheers, > Olli > Am 28.04.2011 17:59 schrieb "Jason Swails" <jason.swails.gmail.com>: >> >> I think I'd tend to agree with Markus on this one (although Ryde's MM/PBSA >> papers use the perl version). I'm not sure how you would go about >> accomplishing the buffer region in the nab program, and I'm pretty sure > Ryde >> et. al. used the nmode program as well. >> >> All the best, >> Jason >> >> On Thu, Apr 28, 2011 at 6:18 AM, Oliver Kuhn <oak.amber.googlemail.com >> wrote: >> >>> Again, Jason, >>> >>> I can remember I have asked something similar few month (or maybe a year > ;) >>> ago. >>> I would like to use the method from: >>> An improved method to predict the entropy term within the MMPBSA > approach, >>> Kongsted Ryde, J Comput Aided Mol Des 2009 >>> >>> The main reason is that it will be more computationally efficient and > I'm >>> interested how the distribution of entropy estimates will be compared to >>> usual NMA. >>> >>> The method minimizes a truncated 8A environment around the ligand but > with >>> a >>> 4A fixed buffer region. >>> Thus, I would tend to input a traj with the 12A environmental residues >>> around the ligand to the NMA routine in the MMPBSA.py script. >>> Can you suggest an easy way to tell the script to keep the 4A buffer > region >>> fixed during minimization - in other words, where do I have to change > the >>> code and set restraints? >>> >>> And b.t.w. thanks also to Bill and Carlo for the discussion on the usage > of >>> internal dielectric 1,2,4. >>> >>> Regards, >>> Oliver >>> >>> -- >>> Oliver Kuhn, Department of Bioinformatics, >>> Center for Medical Biotechnology, University of Duisburg-Essen, >>> Universitätsstr. 1-5, 45141 Essen, Germany >>> phone +49 201 183-3121, oliver.kuhn.uni-due.de >>> _______________________________________________ >>> AMBER mailing list >>> AMBER.ambermd.org >>> http://lists.ambermd.org/mailman/listinfo/amber >>> >> >> >> >> -- >> Jason M. Swails >> Quantum Theory Project, >> University of Florida >> Ph.D. Candidate >> 352-392-4032 >> _______________________________________________ >> AMBER mailing list >> AMBER.ambermd.org >> http://lists.ambermd.org/mailman/listinfo/amber > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Thu Apr 28 2011 - 18:00:02 PDT