Re: Restraints on the outer solutes

From: Vibhor Agrawal (
Date: Mon Dec 28 2015 - 03:50:57 CST

Hi Sakshi:
You need to do it using VMD .change the B factor field using TCL command
line for the pdb region ,create new pdb and psf for same for the system you
want to get restraint on.
Refer to the Membrane protein tutorial on the VMD website.

On Mon, Dec 28, 2015 at 4:39 AM, Diksha Dubey <>

> Hi,
> I have a selected a spherical region of a pdb system (radius 25 Angstrom)
> and solvated this system within a water box. I am trying to put restrain on
> the outer solutes of this system, which fall in the region of 23 to 25
> Angstrom. Can anyone please tell me how this can be done using NAMD? What
> should I write in the configuration file to execute this?
> Grateful for your advice.
> Diksha

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