From: Gadi Oron (gadi_at_proteologics.com)
Date: Thu Dec 11 2003 - 01:51:14 CST
Dear NAMD users,
For the last several days I am attempting to run a simulation
of a Zinc-finger protein. I have followed all the steps in the
tutorials, but in all the combinations I have attempted the
system explodes few steps after the minimization ends.
The errors are various, but the common ones are failure in RATTLE
algorithm and "atoms too fast".
I have put a file containing all the data needed to reproduce the
situation here (http://18.104.22.168/namd_crash.tar.bz2).
The steps that I have done are:
1. Extract from vmd the 4 chains of 1FBV.pdb into chainA.pdb,
chainB.pdb, chainC.pdb and ions.pdb.
2. Use psfgen to patch the needed residues and prepare the PSF:
psfgen < step1.psfgen
3. Run the simulation (equil.conf is the namd config file).
The last step always breaks, no matter what parameters I use (with/wo
water, timestep, rigid bonds, minimizing with fixed backbone)...
Any comment will be greatly appreciated!
-- ================= Gadi ORON, PhD -o- Proteologics ====================== =========== gadi_at_proteologics.com =========== +972 8 9475666 =========== History repeats itself -- the first time as a tragi-comedy, the second time as bedroom farce.
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