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
