VMD-L Mailing List

From: Jennifer Brookes (ucapjcb_at_ucl.ac.uk)
Date: Thu Nov 13 2008 - 04:23:03 CST

Dear all,

Recently I got an error using combine.tcl to embed a protein into a
lipid layer. I contacted the author of the script, with my issue and
received some helpful trouble shooting steps. I include my question and
his response below, in case it is of use to any one else.

Dear Dr. Balabin,

Thank you for making your script combine.tcl available over the web. I
hope you don't mind me emailing you - but I have a problem in using it!

What I would like to do is embed a putative olfactory receptor into a
lipid membrane layer. I have followed the steps you describe at:
http://www.ks.uiuc.edu/Research/vmd/plugins/membrane/
but I get the error:

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
reading structure from psf file protein.psf
psf file does not contain cross-terms
ERROR: Unable to open pdb file protein_aligned.pdb to read coordinates

MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.

temp

MOLECULE MISSING! Use resetpsf to start over.

MOLECULE MISSING! Use resetpsf to start over.
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 LINUXAMD64, version 1.8.6 (April 6, 2007)
Info) Exiting normally.
Couldn't open psf file temp.psf

I saw someone else had a similar problem on the VMD mailing list, and
the advice was to contact the authour, in case the script needs updating
for newer versions of psfgen and VMD. I am using VMD 1.8.6. Please could
you help?

With thanks,
Jennifer

Dear Jennifer,

Thanks for reporting the problem. Your VMD output says that it could not
read the file "protein_aligned.pdb". Possible reasons for that are: 1)
the file does not exist in the working directory; 2) the file is
unreadable ("chmod 644 protein_aligned.pdb" sets the correct
permssions); 3) the PDB file "protein_aligned.pdb" does not match the
structure file "protein.psf"; 4) the topology file that gets read in the
beginning of the "combine.tcl" script does not match the structure file
"protein.psf".

I suggest that you do the following troubleshooting steps:

1) Try to read the coordinate file "protein_aligned.pdb" into VMD: open
the Tk console and type:

    mol load pdb protein_aligned.pdb

2) If that works, try to load _both_ structure and coordinate files:

    mol load psf protein.psf pdb protein_aligned.pdb

3) If that works, check what topology file you used to generate the
structure file "protein.psf". The topology file you use with
"combine.tcl" MUST include all definitions used while creating the
structure file "protein.psf".

If some of the above steps help, please feel free to post this
information at the VMD mailing list.

Best,
Ilya