VMD-L Mailing List

From: Bharat Kumar (bharat.stanam_at_gmail.com)
Date: Sat Dec 04 2010 - 01:42:49 CST

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.