From: James Starlight (jmsstarlight_at_gmail.com)
Date: Wed Apr 09 2014 - 09:07:28 CDT
Dear Namd Users!
I have problems of the simulation of my protein-ligand water-soluble
system. First I've simulated apo form of my protein. Than I've took final
conformation from that run and using autpdock I've placed ligand within the
protein's interior re-solvable my system and run energy minimization. This
minimization run produced errors like ( I've used such conf file for any
other systems taking it from the Namd tutorial and have not any problems):
MINIMIZER RESTARTING CONJUGATE GRADIENT ALGORITHM DUE TO POOR PROGRESS
LINE MINIMIZER REDUCING GRADIENT FROM nan TO nan
PRESSURE: 6 -nan -nan nan nan -nan nan nan -nan -nan
GPRESSURE: 6 -nan -nan -nan -nan -nan -nan -nan -nan -nan
ENERGY: 6 9999999999.9999 9999999999.9999 9999999999.9999
9999999999.9999 9999999999.9999 9999999999.9999 0.0000
0.0000 0.0000 9999999999.9999 0.0000 9999999999.9999
9999999999.9999 0.0000 9999999999.9999 9999999999.9999
1065900.0000 9999999999.9999 9999999999.9999
MINIMIZER RESTARTING CONJUGATE GRADIENT ALGORITHM DUE TO POOR PROGRESS
LINE MINIMIZER REDUCING GRADIENT FROM nan TO nan
I've tried to run it on gpu and cpu namd version but result was the same.
How it could be fixed ?
Thanks for help,
James
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