AMBER: Frozen at Minimization

From: Steve Seibold <>
Date: Tue, 19 Dec 2006 09:18:21 -0500


I am attempting an energy minimization on a large protein ( greater than
1000 residues). When I do energy minimization without any restraints
AMBER does minimize the structure although it takes a while (running
maxcycle=200). However, when I put in restraints on the backbone (100
kcal/mol) something weird starts to happen. AMBER, with restraints
applied, runs but seems to "freeze" up in the sense that I have been
running minimization for over 24 hours and the output file still reads
the same as it read just a few minutes into the calculation. It freezes
at the point where it lists the group and number of atoms for restraint.
Does this mean that AMBER is frozen at a step in the calculations? I am
afraid that this is a response in AMBER due to very high potential
energy values. Is this correct?


Thanks, Steve


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Received on Wed Dec 20 2006 - 06:07:43 PST
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