[AMBER] loop relaxation with les

From: Simon Becker <simon.becker.uni-konstanz.de>
Date: Sun, 26 Sep 2010 16:34:06 +0200

  Hi all,

I'm working with a small protein bound to a transmembrane receptor.
Unfortunately we are unable to crystallize the receptor alone, most
likely because the long loops connecting the tm-helices are interfering
with the crystal packing.
To produce a relaxed structure of the receptor alone I considered using
LES on these loops as the tm-region should be quite rigid. I put all
interesting loops into one subspace and made 5 copies, like that:

omas
spac numc=5 pick #mon 404 445 | #mon 600 650 | #mon 542 576 | #mon 479
503 done

is this even smart?
Are there methods better suited for this?

Addless however finished without errors after I increased a few
parameters and recompiled.

sander.LES.MPI stops with this error:

  LES parameters were found
  EXCEEDED MAXLESADJ!

I found that maxlesadj is a prameter set in several .f and .h files to
3.000.000. This looks sufficient for my task, and I'm reluctant to
temper with it.
Does this mean there is a problem with my inputfiles?
Is there any documentation concerning the les flags in the prmtop file?

help please!
simon

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Received on Sun Sep 26 2010 - 08:00:04 PDT
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