VMD-L Mailing List

From: Marcos Sotomayor (sotomayo_at_ks.uiuc.edu)
Date: Thu Mar 23 2006 - 22:13:15 CST

Hi Rima,

As pointed out in the NAMD tutorial (look at the box "Multiple Chains"
under section "Creating a Protein Structure File") you need to create
multiple segments, each from a different pdb file, in order to deal with
proteins that have multiple chains. In your case, you would need to first
create a pdb file for each of your three chains (lets say A.pdb, B.pdb,
and C.pdb; you may want to use the commands specified in the tutorial to
create these files) and then, within psfgen, create 3 separate segments:

segment A { pdb A.pdb }
coordpdb A.pdb

segment B { pdb B.pdb}
coordpdb B.pdb

etc.

Have a look at the psfgen user's guide for more details
(http://www.ks.uiuc.edu/Research/vmd/plugins/psfgen)

Note that you can skip all those steps by using the new AutoPSF plugin,
which will build the psf file automatically for you.

Marcos

On Thu, 23 Mar 2006, Rima Chaudhuri wrote:

> Hi,
>
> I am trying to generate a psf file of a protein with 3 chains. On
  following the tutorial instructions of using the command 'segment U ....'
  it just choses one of the chains(but I want it to read all the 3 chains),
  moreover it gives an error for every residue that it reads from the pdb
  file. On loading the resuting psf and pdb files that i creates, there are
  astray residues far off from the protein chain (last 2 residues).
> If I use just 1 chain as the input pdb file, it does not give any
  error but on trying to set coordinates via command:
> coordpdb sarsp_A.pdb U
> It gives the following error.
> Warning: failed to set coordinate for atom CG2 VAL:301 U for every
residue respectively.
>
> Please let me know :
> 1)what needs to be done if I want to use all 3 chains
> 2)how to get rid of these errors.
>
> Thanks
> -Rima
>
>
> ---------------------------------
> New Yahoo! Messenger with Voice. Call regular phones from your PC for low, low rates.