AMBER Archive (2006)

Subject: AMBER: restraint=0.0000 during minimization?

From: Evan Kelly (ebkelly_at_ualberta.ca)
Date: Thu Aug 03 2006 - 12:48:17 CDT

Hi Everyone,

I am trying to use group inputs to restraint two sections of a
protein during a minimization. The output file states that two
groups with harmonic restraints are found and the correct number of
atoms is found for each group so I assumed that everything was
working fine. However, the output gives the restraint energy as
"restraint=0.0000" at every step, and this concerns me. Here is my
input file:

Minimization
&cntrl
   imin = 1,
   drms = 0.0001
   ntmin = 1,
   ncyc = 250,
   maxcyc = 1000,
   ntb = 0,
   ntf = 1,
   ntc = 1,
   cut = 30,
   ntr = 1,
   igb = 2, saltcon= 0.1, rgbmax = 30, gbsa = 1,
   ntpr = 1, ntwx = 100, ntwr = 100,
/
HOLD THE BINDING DOMAIN FIXED
10.0
RES 611 616
END
HOLD THE BINDING DOMAIN (2nd part) FIXED
10.0
RES 643 664
END
END

Can anyone comment on this? Thanks!

----------------------------------
Evan Kelly
ebkelly_at_ualberta.ca

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