Custom Search
-- Sally Pias Postdoctoral Fellow Stony Brook University On Mon, Nov 30, 2009 at 5:03 AM, Anna Reymer <reymer.chalmers.se> wrote: > Dear All, > I have the following problem. > When I try to run MD where I use my complex.rst as an input coordinates file and Sander produces no output files, neither trajectory file, nor restart file and the out file is just empty. > > I have tested the input and topology files and they are fine, and the problem seems to be in the restart file. > > I produce the restart file from a trajectory file, using ptraj script: > > trajin md_2_complex.mdcrd 4243 4243 > trajout complex.rst restart nobox append > > I guess the problem is in initial rst file, which, for some strange reason, contains just columns of zeroes in the second half. > > Has anybody any advice? Thanks in advance. > > Regards, > Anna > > ----------- > Anna Reymer, PhD student > Physical Chemistry, > Department of Chemical and Biological Engineering > Chalmers University of Technology > Kemivägen 10 > SE-412 96 Gothenburg > Sweden > > Phone: +46-(0)31-7722815 > _______________________________________________ > 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 Mon Nov 30 2009 - 11:30:04 PST