VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Mon Nov 09 2009 - 14:06:44 CST

Perhaps naive question as I don't know NAMD yet.

I have applied the PSF Builder and CG Builder to a multimeric protein,
apparently successfully: the cg pdb loads correctly, no clashes or
contacts. However, I noticed that the TER lines that separate the
subunits, and renumbering from residue #1of each subunit of the input
.pdb, have not been maintained. Consecutive numbering of all residues
makes practical problems in dealing with the ensemble, therefore, is
any way to get the pdb with separate residue numbering for each
subunit? I am slowly organizing to carry out CG MD simulations with
NAMD, which I never used before.

thanks
francesco pietra