geometry deformation

From: lecan (
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

 Luis L.

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