the restraints look ok, but maybe one of the other
energy terms is very high. can you send the full energy
output from step 0? also send your md.ntr.in so we
can see what you're trying to do. for example, are you
using ntr=1?
also, tell us some more details- have you done energy
minimization on the system? equilibration? in other
words, how did you get the input coordinates for this
simulation?
Carlos
----- Original Message -----
From: "RAJA SWAMINATHAN" <genes2000_in.yahoo.com>
To: <amber.scripps.edu>
Sent: Monday, November 24, 2003 9:47 AM
Subject: AMBER: protein MD - problem
> Dear amber usrs
>
> I am trying to do MD on a quite big protein roughly
> ~200 AA residues. I am getting this error in the
> md.ntr.in part
>
> NMR restraints for step 0
> Energy (this step): Bond = 0.000 Angle =
> 0.000 Torsion = 0.000
> Energy (tot. run) : Bond = 0.000 Angle =
> 0.000 Torsion = 0.000
>
> DEVIATIONS: Target=(r2+r3)/2
> Target = closer of r2/r3
> This step Entire run This
> step Entire run
> ave. rms ave. rms ave.
> rms ave. rms
> Bond 0.000 0.000 0.000 0.000 0.000
> 0.000 0.000 0.000
> Angle 0.000 0.000 0.000 0.000 0.000
> 0.000 0.000 0.000
> Torsion 0.000 0.000 0.000 0.000 0.000
> 0.000 0.000 0.000
>
============================================================================
===
> vlimit exceeded for step 0; vmax = 15176.441
>
> COORDINATE RESETTING CANNOT BE ACCOMPLISHED,
> DEVIATION IS TOO LARGE
> NITER, NIT, LL, I AND J ARE : 0 0 13 33
> 35
>
> FATAL ERROR
>
> i have tried to run the input by increasing the vlimit
> it didn't helped me. then i tried by reducing the
> weight, it also didn't worked. is it advisable to
> change the *.h file in amber to increase the max no of
> bp
>
> Thanks for ur kind help
>
> Sincerely
> Raja Swaminathan
>
>
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Received on Mon Nov 24 2003 - 15:53:01 PST
