Re: geometry deformation

From: Grace Brannigan (
Date: Wed Mar 07 2012 - 15:45:36 CST

Hi Luis,

Did you use the $sel writepsf <filename> command in VMD to create your psf,
rather than writepsf within psfgen? The former command will write a psf
without angles and dihedrals specified, which is no good for simulation,
and which will yield the result you mention.


On Wed, Mar 7, 2012 at 4:10 PM, lecan <> wrote:

> 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.

Grace Brannigan
Assistant Professor
Center for Computational and Integrative Biology (CCIB) &
Department of Physics
Rutgers University, Camden, NJ

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