VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Sun Oct 14 2007 - 03:23:23 CDT

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.

       
____________________________________________________________________________________
Yahoo! oneSearch: Finally, mobile search
that gives answers, not web links.
http://mobile.yahoo.com/mobileweb/onesearch?refer=1ONXIC