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-- Department of Molecular Therapeutics The Scripps Research Institute On 5/21/10 3:01 PM, "case" <case.biomaps.rutgers.edu> wrote: On Fri, May 21, 2010, Douglas Kojetin wrote: > Setting pencut = -1.0, here are the first few distance restraints: > > --------------------------------------------------------------------------- > --- > First atom Last atom curr. value target deviation penalty > --------------------------------------------------------------------------- > --- > HA VAL 49 -- H LYS 52: 3.143 4.610 1.467 0.000 d > 13: 0 OK...now we have progress; you can examine the input data in the RST file, looking just at the first restraint. If the solution is not obvious, you could post just that one piece of input and ask questions. Also, check your mdin file to make sure you have not set some restraint weight to zero. Not to beat a dead horse, but my previous suggestion of setting LISTIN=POUT still seems like a good idea -- it gives lots more detail about what is going on. I think it is rather unlikely that this is related to serial vs. parallel, or would be fixed by some recompilation. There are lots of ways that restraints can do things you don't expect, but difficult to remotely debug without more information. (We would need to know r1,r2,r3,r4, rk2, rk3 at a minimum.) ....dac _______________________________________________ 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 May 27 2010 - 09:00:06 PDT