From: Chitrak Gupta (
Date: Wed Jun 01 2016 - 08:57:57 CDT

Hi Srijita,

Have you looked at the file PSF/PDB file? If the number of atoms is what
you expect it to be, then your system does have all 5 proteins. In that
case, what is happening most likely is, VMD is superimposing all 5 of your
proteins (because all of them have the exact same coordinates), so you are
only seeing one.

To get around this, give different chain name to the 5 proteins. You can
then select them separately using atomselect, and move them around using
moveby command. However, how you move them will depend on the details of
your system and what you want to simulate.

Hope this helps,

On Tue, May 31, 2016 at 6:03 AM, Srijita Paul <> wrote:

> Hi
> I have prepared a system with 5 protein (all r same protein) and tip3p
> water using packmole.i have also generated psf file using psfgen.the final
> pdb created by psfgen contains 5 proteins but when it is being uploaded to
> vmd its only showing 1 protein segment.i have taken different segments for
> each of the 5 protein during running psfgen.
> please give me solution how can i make psf for a system containing more
> than 1 protein.

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