VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Dec 06 2010 - 09:31:05 CST

In order to help, you people will need to be able to see what your
.pgn file actually contained. There is obviously an error of some
kind in your script, but without seeing it, we can't possibly guess
what it is.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Sat, Dec 04, 2010 at 02:42:49AM -0500, Bharat Kumar 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. 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
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