VMD-L Mailing List

From: Roman Petrenko (rpetrenko_at_gmail.com)
Date: Mon Nov 09 2009 - 15:01:26 CST

So, i don't understand, why can't you split your protein into one
monomer per file and then build the model and assemble everything
afterwards.

On Mon, Nov 9, 2009 at 3:06 PM, Francesco Pietra <chiendarret_at_gmail.com> wrote:
> 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
> 

-- 
Roman Petrenko
Physics Department
University of Cincinnati