Hi Anamika,
A restraint_wt of 500.0 is probably a little high. Try reducing this to 50.0
or so. Also we'd need to see the output file in order to be able to comment
on why the code segfaults. We'd also need details about your machine, the
version of sander you are using, if you applied the bug fixes, what compiler
you used and how you ran it (serial /parallel etc).
All the best
Ross
From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of
Anamika Awasthi
Sent: Tuesday, April 29, 2008 4:44 AM
To: amber.scripps.edu
Subject: AMBER: segmentation fault in SANDER
Dear Friends,
Thanks for your guidance.
I created min,in file and gave this--
initial minimization with Cartesian restraints for the solute
&cntrl
imin=1, maxcyc=200,
ntpr=5,
ntr=1,
restraint_wt=500.0,
restraintmask=':1-1944',
/
my protein is hexamer and wants to fix whole protein as I wants to do energy
minimization for solvant only.
but sander is not running properly and showing segmentation fault..why this
is so?
Thanks in advance
--
Anamika Awasthi
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Received on Wed Apr 30 2008 - 06:07:46 PDT
