From: lecan (lecan_at_ibt.unam.mx)
Date: Wed Mar 07 2012 - 15:10:27 CST
Hi everybody!
I Have been trying to simulate a protein-DNA system, but something is
wrong with the psf file or with NAMD parameters and I have been unable
to find the problem. When I make the psf and pdb files with VMD,
everything looks OK, including geometry of bonds and atom distribution.
Nevertheless, during system minimization this geometry is affected
immediately (at the first steps), showing planar deformation of nucleic
bases and histidines and the normal positions of hydrogens are loosed
almost completely, adopting strange angles of the bonds. If anybody has
any idea or has passed through this problem, please feel free to speak
(joke!).
Luis L.
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