VMD-L Mailing List

From: Bharat Kumar (bharat.stanam_at_gmail.com)
Date: Sun Dec 05 2010 - 22:40:28 CST

Hi

I figured out that I wrongly copied the command "coordpdb" as "coord". Sorry
for the silly mistake!

Bharat.

On Sat, Dec 4, 2010 at 2:42 AM, Bharat Kumar <bharat.stanam_at_gmail.com>wrote:

> Hi
>
> I am new to molecular simulations using VMD. I am first trying to embed my
> transe membrane Na/K ATPase into a POPC membrane. I am following the
> "Membrane Protein Tutorial".
>
> As a first step I am generating .psf for the protein. I have followed the
> instructions given in the first chapter of the tutorial. But I end up in
> getting the error message:
>
> arguments: segid resid atomname { x y z }
> MOLECULE DESTROYED BY FATAL ERROR! use resetpsf to start over.
>
> Can you please explain why am I encountering this message?
>
> The protein is a trimer with an alpha, beta and gama subunits. I am only
> interested in alpha subunit. So I have created a segment-A.pdb with
> co-ordinates of alpha subunit. As psf needs non-covalently bound structures
> separately I made a separate pdb files for alpha unit, potassium ions and
> crystallographic waters using tcl scripts in the tutorial. Finally I wrote
> .pgn file to generate pdb and psf files. But I am stuck with the above
> error. Please suggest me where I may possibly doing wrong.
>
> Thanking you,
> Bharat.
>
>
>