From: gurunath katagi (gurukatagi_at_gmail.com)
Date: Fri Aug 28 2009 - 00:16:01 CDT
i know this question has been asked by many a times in the mailing
list..,but still i have a doubt in this..
when i run the minimization and equilibriation of protein and ligand bound
to it.. i have fixed the protein and allowed only the ligand to move first
(fixedfile -- protein file)
but i am getting the following error;
WRITING VELOCITIES TO RESTART FILE AT STEP 5000
FINISHED WRITING RESTART VELOCITIES
REINITIALIZING VELOCITIES AT STEP 5000 TO 310 KELVIN.
TCL: Running for 500 steps
ERROR: Constraint failure in RATTLE algorithm for atom 9080!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Exiting prematurely.
*when i see the trajectory , i observe that the 9080 atom does not show any
movement at all...............,
now my question is why does that atom soes not move eventhough the beta
factor is set 0. and how do ifix the problem?
-- Gurunath M Katagi Graduate Student Supercomputer Education and Research Center Indian Institute Of Science Bangalore
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