RE: AMBER: rgbmax--something wrong with my input file?

From: Ross Walker <ross.rosswalker.co.uk>
Date: Tue, 27 Jun 2006 15:52:06 -0700

Hi Kenley,
 
You have something very wrong with your starting structure:
 
  NSTEP ENERGY RMS GMAX NAME NUMBER
      1 6.8283E+12 4.3714E+11 3.8864E+13 CD 6756
 
 BOND = 55589.4701 ANGLE = 12184.7419 DIHED =
24774.6027
 VDWAALS = ************* EEL = -179753.6450 EGB =
-38256.1350
 1-4 VDW = 2621189.7868 1-4 EEL = 113699.2076 RESTRAINT =
0.0000

 
Note the *****'s in the VDWAALS term, this means the number is too large to
fit in the output space, plus your BOND energy is huge as is your 1-4 VDW
energy. You will need to work out what is wrong with this and fix this. You
probably have 1 or more atoms sitting on top of each other. I would start by
looking at atom 6756 (CD) as this is reported to have the biggest force on
it which is 3.886 * 10^13!!!! KCal/mol/A. This is HUGE... Anything else past
this point in the output file is pretty much meaningless as there is no way
the minimiser can cope with such a strained system.
 
As for the second problem with RGBMAX I cannot see anything obviously wrong
with your input file but you could try specifying the values that are floats
as floats instead of integers. I.e. rgbmax=30.0 rather than just 30. Same
with cut, and restraint_wt. You might also have some strange line endingings
in your file. Try creating a brand new file and typing in the options again.
On another note a restraint_wt of 500.0 is probably way too much. You can
get away with this for minimisation but it would be way too high for MD. Try
a value of 10.0 or so, you may get better results. You still need to fix
your input file first though.
 
All the best
Ross

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  _____

From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of
Kenley Barrett
Sent: Tuesday, June 27, 2006 14:10
To: amber.scripps.edu
Subject: AMBER: rgbmax--something wrong with my input file?


Dear AMBER community,

I am having problems running a simple implicit solvent minimization. I have
tried to run the job on two different computers. On the first computer, the
job completed but produced a very strange .out file in which, after a point,
the energy began rotating between -1, -9, and -3. I have attached this .out
file. On the second computer the job crashed with the error: " The NAMELIST
READ statement cannot be completed because item rgbmax is not a member of
the NAMELIST group cntrl. The program will recover by
discontinuing further processing of the READ statement..."

I have examined my .in file and I can't figure out how I used "rgbmax"
incorrectly, or what else I might have done wrong. If anyone could offer any
advice on what mistake I have made, I would be very grateful. My .in file is
pasted below.

Thank you in advance.

Kenley

&cntrl
  imin=1,
  ntx=1,
  ntf=1,
  ntb=0,
  cut=35,
  igb=5,
  rgbmax=30,
  ntr=1,
  ntc=1,
  maxcyc=500,
  ntmin=2,
  restraint_wt=500,
  restraintmask=:* & !.H= & !:WAT
 /






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Received on Wed Jun 28 2006 - 06:07:08 PDT
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