From: ELENA JEAN LEVIN (ejlevin_at_wisc.edu)
Date: Thu Nov 06 2003 - 13:45:19 CST
Hi,
I'm a new NAMD user trying to run a simple
minimization and equilibration of a kinase in a
water box, using the online tutorial as a guide as
well as the help of another student who has
attended the summer workshop at IUIC. We first ran
the simulation with the protein fixed and only the
water molecules moving, and did not encounter any
problems. However, when we then tried continuing
with both the protein and water molecules unfixed,
we kept getting a "constraint failure in RATTLE
algorithm" error message for the same ten atoms
each time. We've tried the two suggestions given
in the namd-l archive to someone experiencing a
similar problem, increasing the boundary sizes and
increasing the number of minimization steps, but
to no effect. We had the same problem with the
ubiquitin tutorial, even though the grad student
I'm working with swears he's following the exact
same steps as at the UIUC workshop. Does anyone
have an idea as to what could be going wrong?
We've put the log, configuration and other files
that we're using online:
<a
href="http://www.sit.wisc.edu/~rmbannen/namd/waku.conf">configuration
file</a>
<a
href="http://www.sit.wisc.edu/~rmbannen/namd/waku.log">log
file</a>
<a
href="http://www.sit.wisc.edu/~rmbannen/namd/wak.psf">Solvated
AK psf</a>
<a
href="http://www.sit.wisc.edu/~rmbannen/namd/wak_out4.pdb">Solvated
AK pdb</a>
Thanks,
Elena Levin
Department of Biochemistry
University of Wisconsin, Madison
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