AMBER Archive (2008)

Subject: AMBER: LINMIN error in geometrically constrained minimization @ MM-PB/SA conditions

From: Alexander Metz (
Date: Thu Dec 04 2008 - 11:04:03 CST

Hello everybody, I am trying to minimize a small molecule while applying the PB continuum model and a couple of conformational restraints on torsion angles. The minimization output contains this: ### .... RESTARTED DUE TO LINMIN FAILURE ... for a couple of times. and complains a lot about ### PB Warning in epsbnd(): No neighbor found for boundary grids total: 6 with changing numbers. However the minimization goes on (or restarts) until it finally ends with ### .... RESTARTED DUE TO LINMIN FAILURE ... ### ***** REPEATED LINMIN FAILURE ***** ### ***** SEE FOR MORE INFO ***** folowed by the final RESULTS and TIMINGS section. It does not seem like the minimization converged at this stage. Minimizing the produced restart file again results in an significant energy reduction. The calculation stops during the conjugate gradient part. Steepest descent minimization is not interupted. I read that this could be caused by artifical displacement or closeness of atoms in a simulation, but this is not the case in the final structure. Neither do I use SHAKE. Do you have any ideas what could be wrong ... or how to do an energy minimization with an effective energy funktion equal to the one used by MM-PB/SA for single point energy calculations? All files needed for the calculation are in the attachement. Thanks a lot, Alexander

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