AMBER Archive (2003)

Subject: AMBER: protein MD - problem

From: RAJA SWAMINATHAN (genes2000_in_at_yahoo.com)
Date: Mon Nov 24 2003 - 08:47:53 CST

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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