AMBER Archive (2003)

Subject: angle violation in SANDER simulation

From: XU Xingfu (scip1190_at_nus.edu.sg)
Date: Wed Jun 04 2003 - 04:11:24 CDT

Hi, everyone,
          I am beginning to learn use AMBER 7 to do energy minimization of
my protein structure after the NMR calculation by CYANA. I used the 15ps
simulated annealing protocol without any change of the parameters according
to the tutorial. The final summary file says that there are some angle
restraints violations ( > 5 and even 50). The distance restraints have no
large violation( < 0.25). But using the same restraints files, CYANA
calculation will not generate any angle violation( > 5). The angle
violations generated during AMBER refinement are in the loop regions where I
only set some very loose restraints by TALOS prediction.
         I am trying to fix the problem. You suggestions and answers are
greatly appreciated.