From: Dong Luo (us917_at_yahoo.com)
Date: Thu Jul 28 2011 - 12:21:28 CDT
The FEP simulation is on a mutation from TYR to ALA. The mutated residue is surround by other residues. Upon continue from restart files, the simulation immediately complained with "ERROR: Constraint failure in RATTLE algorithm for atom ####". Check the protein in VMD show that some of the TYR atoms are within 1 angstrom of atoms from surrounding residues. Is this normal as TYR is disappearing during the simulation? But how can a restart get over with that ERROR. It looks to me the simulation runs without problem before the restart point with the same situation. The configuration file for restart is following previous posts in this mailing list.
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