Hi, I am running a sander.MC calculation of protein/ligands
interactions with 10 ligands . My calculation can't go through.
...
I note that you're starting with a 'cold' system (no velocities),
running with a conservative timestep, starting a bit warm at 100K
target temp,
ntc=2, ntf=1,
(normally ntf would = ntc)
In the output we see that there is a problem with the starting setup:
electrostatic & vdw are 'off the map', which indicates that atoms are
superimposed.
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Output
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NSTEP = 1 TIME(PS) = 0.001 TEMP(K) = 0.00 PRESS = 0.00
Etot = nan EKtot = 0.0000 EPtot = nan
BOND = 565.0527 ANGLE = 1790.4638 DIHED = 1746.6942
1-4 NB = 1783.7010 1-4 EEL = 12299.8193 VDWAALS = nan
EELEC = nan EHBOND = 0.0000 CONSTRAINT = 0.0000
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Received on Wed Sep 26 2001 - 17:34:45 PDT
