Re: regarding protein-dna complex simulation

From: Leonardo Trabuco (
Date: Fri Dec 19 2008 - 21:08:15 CST

Again, please keep the discussion in the namd-l list.

On Fri, Dec 19, 2008 at 8:54 PM, prasun kumar <> wrote:
> I have tried by using single residue also,for this also I am getting the
> same error.You are telling me to add 'regenerate angles dihedrals'.Is it
> after the patches or some where else.

Yes, after patches.

> One more thing the error is telling
> about the dihedral angle,which doesnot exist.It is the dihedral between H2'
> C2' C1' N3.It can not be formed(correct me if I am wrong).

It's hard to tell, since the atom types could correspond to many
different atoms.

What is the output of psfgen? Do you see any errors? Did you look at
the generated .psf and .pdb files in VMD?

If you want, you can send me the pdb file for the single nucleotide
you used along with the script and I'll take a look at it.


Leonardo Trabuco, Ph.D. candidate
Theoretical and Computational Biophysics Group
University of Illinois at Urbana-Champaign

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