From: Peter Spijker (pspijker_at_wag.caltech.edu)
Date: Wed May 19 2004 - 18:30:57 CDT
Hi all!
At this very moment I am trying to adapt the top_whatever.inp and
par_whatever.inp files so I can run a protein structure with different
ligands, either antagonists or agonists. So far so good I managed to get two
structures right (well, it worked, if it worked needs to be find out yet).
These are for epinephrine and norepeniphrine. Now I am working on butoxamine
(a antagonist), but I encounter some problems. This time no psfgen
problems, but something I do not understand from NAMD. The program does not
complain about any missing parameters or something alike, but when running a
minimisation it sends as output only this:
INITIAL STEP: 1e-06
GRADIENT TOLERANCE: nan
BRACKET: 0 0 nan nan nan
RESTARTING CONJUGATE GRADIENT ALGORITHM
INITIAL STEP: 2.5e-07
GRADIENT TOLERANCE: nan
BRACKET: 0 0 nan nan nan
RESTARTING CONJUGATE GRADIENT ALGORITHM
And so on, and so on.Only the initial steps become smaller and smaller.
Untill it fails and the program stops without writing any file information.
Which seems okay, because the simulation actually never started. I do not
get what might be wrong. The initial energies look not too bad:
TCL: Minimizing for 2000 steps
ETITLE: TS BOND ANGLE DIHED IMPRP
ELECT VDW BOUNDARY MISC KINETIC
TOTAL TEMP TOTAL2 TOTAL3 TEMPAVG
ENERGY: 0 37.5420 544.9918 0.1572 0.0000
54.5077 11.1455 0.0000 0.0000 0.0000
648.3442 0.0000 648.3442 648.3442 0.0000
Can anyone give me a clue what might be going on? It would be very helpful I
think. Thank you all.
Kind regards,
Peter Spijker
--- Peter Spijker Fulbright Fellow - The Netherland-America Foundation California Institute of Technology Biochemistry & Molecular Biophysics Materials Process and Simulation Center MC 139-74 Caltech Pasadena, CA-91125 The United States of America Phone: (626)-395-2844 E-mail: pspijker_at_wag.caltech.edu
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