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-- Jason M. Swails Quantum Theory Project, University of Florida Ph.D. Candidate 352-392-4032 On May 29, 2011, at 1:35 PM, Andrew Voronkov <drugdesign.yandex.ru> wrote: > Dear Amber developers, are there any shifts in this question? > I need to remove water from dataset of PDB files and it would be better to do this through modeification of the shell script just by adding -nowat flag to ambpdb rather than stripping water from prmtop, rst or mdcrd files. > Maybe there are any scripts for this in the community now? > > Best regards, > Andrew > > 06.12.2009, 10:09, "Bill Ross" <ross.cgl.ucsf.edu>: >>>> maybe it s posible to strip waters from .rst file and then convert >>>> it to PDB. >>> Ideally someone (it could be you) would add a -nowat option to >>> ambpdb to do the right thing. >> >> PS - stripping from rst means you'd have to generate the no-wat >> prmtop for ambpdb to work with the modified rst. Making the change >> to ambpdb is more sensible I think. While at it, a -nosolvent flag >> could strip whatever prmtop thinks is solvent (there is a pointer >> to the solvent section as I remember), which might provide >> the convenience of leaving in xtal waters. >> >> Bill >> >> _______________________________________________ >> 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 Sun May 29 2011 - 20:00:02 PDT