From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Oct 17 2007 - 22:11:59 CDT

Dear Francesco,
  I believe The "cross term" error messages are all from psfgen.
I'm not sure what "combine.tcl" script you're running, but
you're going to have to look at it closely and see if what it is trying
to do even makes sense for the data files you're working with.
If this is one of the scripts from the CTBP workshop (I turned
up one script by that name in an tutorial by Richard Law),
I'd suggest emailing the author of the tutorial/script and
checking if you're using it correctly, or whether the script
may need to be updated for the newer versions of psfgen and VMD.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Sun, Oct 14, 2007 at 01:23:23AM -0700, Francesco Pietra wrote:
> New to embedding a protein in a POPC bilayer with VMD 1.8.6. Perhaps, instead
> of loosing your time to examine my faulty doing, I should be directed to a
> complete tutorial that I was unable to find. At any event, what I did:
>
> 1) With membrane plugin I got membrane.pdb and membrane.psf, apparently
> smoothly.
>
> 2)With psf plugin (Main menu > Extensins > Modeling > AutoPSF Builder) from
> myprotein.pdb I created newmyprotein.pdb and newmyprotein.psf (by hitting "I'm
> feeling lucky" first at Step 1, then at Step 3, which were the only one active
> sections).
>
> 3) Loaded membrane.pdb and newmyprotein.pdb and adjusted the protein into lipid
> with VMD main > Mouse > Move > Molecule. Then saved
> coordinates for the protein as pdb file.
>
> 4) Downloaded scripts combine.tcl and top_all27_pro_lipid.inp into the working
> directory.
>
> 5) vmd -dispedev text < combine.tcl | tee combine.log
>
> reported "top molecule missing". The log (shown below) reveals that psf files
> could not be read because lacking "cross terms" (which I don't understand).
>
> Thanks
> francesco pietra
>
> Info) VMD for LINUX, version 1.8.6 (April 6, 2007)
> Info) http://www.ks.uiuc.edu/Research/vmd/
> Info) Email questions and bug reports to vmd_at_ks.uiuc.edu
> Info) Please include this reference in published work using VMD:
> Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
> Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
> Info) -------------------------------------------------------------
> Info) Multithreading available, 1 CPU detected.
> Info) Free system memory: 822MB (81%)
> on
> 1.4.5
> reading topology file top_all27_prot_lipid.inp
>
> >>>>>> Combined CHARMM All-Hydrogen Topology File for <<<<<<<<<
> >>>>>>>>> CHARMM22 Proteins and CHARMM27 Lipids <<<<<<<<<<
> from
> >>>>>>>>CHARMM22 All-Hydrogen Topology File for Proteins <<<<<<
> >>>>>>>>>>>>>>>>>>>>> August 1999 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<
> >>>>>>> Direct comments to Alexander D. MacKerell Jr. <<<<<<<<<
> >>>>>> 410-706-7442 or email: alex,mmiris.ab.umd.edu <<<<<<<<<
> and
> \\\\\\\ CHARMM27 All-Hydrogen Lipid Topology File ///////
> \\\\\\\\\\\\\\\\\\ Developmental /////////////////////////
> Alexander D. MacKerell Jr.
> August 1999
> All comments to ADM jr. email: alex,mmiris.ab.umd.edu
> telephone: 410-706-7442
>
> Created by CHARMM version 27 1
> clearing structure, preserving topology and aliases
> reading structure from psf file membrane.psf
> psf file does not contain cross-terms
> reading coordinates from pdb file membrane.pdb
> ERROR: Unable to open psf file protein.psf
> MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.
>
> MOLECULE MISSING! Use resetpsf to start over.
>
> temp
>
> MOLECULE MISSING! Use resetpsf to start over.
>
> MOLECULE MISSING! Use resetpsf to start over.
> Couldn't open psf file temp.psf
> ERROR) Could not read file temp.psf
> Unable to load structure file temp.psf
> There is no 'top' molecule in atomselect's 'molId'
> can't read "sellip": no such variable
> can't read "lseglist": no such variable
> -55
> 41
> -51
> 34
> There is no 'top' molecule in atomselect's 'molId'
>
> MOLECULE MISSING! Use resetpsf to start over.
>
> MOLECULE MISSING! Use resetpsf to start over.
> Info) VMD for LINUX, version 1.8.6 (April 6, 2007)
> Info) Exiting normally.
>
>
>
>
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-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078