Re: AMBER: restraint value: written but none specified

From: Ben Sattelle <>
Date: Fri, 20 Apr 2007 22:51:30 +0100

prior to this was minimisation,

  imin=1, maxcyc=1000, ncyc=1000, cut=9.0,

in which RESTRAINT=0.0 for previous runs and RESTRAINT=non-zero for the one in
question, again, this input has been used for previous runs where
was printed.

diff'ing mini.inp (above) and *.mdin (posted previously) for both cases yeilds
no difference. Is is possible the non-zero restraint arrises from the prmtop
and inpcrd files?

the only difference in setup was the use of solvatecap to place 1 water
in 'gap' created by amino acid mutation of M->A and M->G. appart from the
mutations (implemented in the pdb file) and the additional water molecule the
inputs are identical. thanks for your prompt reply, Ben.

> Ben Sattelle wrote:
>> Dear list,
>> output includes a restraint value although none were specified (ntr=0),
>> `EAMBER (non-restraint)` and `RESTRAINT` values have not been
>> written to output
>> for previous runs using this input, any feedback on possible reasons
>> for this
>> gratefully recieved. Best wishes, Ben.
> Did you check that the input values echoed in your output file are
> identical to those in prior output files? You might clip out the
> opening section of a "good" and "bad" output file, where the input
> options are listed, and run diff on these excerpts.
> I suspect you may find a change in the opening of the output files
> that will explain the trouble - and the inputs will not be what what
> you thought they were, after all.
> C

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Received on Sun Apr 22 2007 - 06:07:49 PDT
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