Re: problems with combine.tcl

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Thu Oct 09 2008 - 14:19:19 CDT

On Wed, 8 Oct 2008, jose correa wrote:

JC> Dear all
JC> I prepare pdb/psf for both protein and membrane as well as the
JC> combine.tcl script
JC> So, enter this information: vmd -dispdev text < combine.tcl |tee combine.log
JC> bu it show:

how about _reading_ the output instead of reposting
the same question again?

JC> August 1999 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<
JC> >>>>>>> Direct comments to Alexander D. MacKerell Jr. <<<<<<<<<
JC> >>>>>> 410-706-7442 or email: alex,mmiris.ab.umd.edu <<<<<<<<<
JC> and
JC> \\\\\\\ CHARMM27 All-Hydrogen Lipid Topology File ///////
JC> \\\\\\\\\\\\\\\\\\ Developmental /////////////////////////
JC> Alexander D. MacKerell Jr.
JC> August 1999
JC> All comments to ADM jr. email: alex,mmiris.ab.umd.edu
JC> telephone: 410-706-7442
JC>
JC> Created by CHARMM version 27 1
JC> clearing structure, preserving topology and aliases
JC> reading structure from psf file membrane-80.psf
JC> Error processing dihedrals

so something is going wrong here. most likely your
membrane-80.psf file is not correct. since you provide
no information to reproduce your problem, you'll have
to debug the script yourself by executing the steps in
your combine.tcl step by step to identify where it breaks.

the rest of the error messages are just consequences of
the first error and have no relevance (for now).

cheers,
   axel.

JC>
JC> MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.
JC>
JC> MOLECULE MISSING! Use resetpsf to start over.
JC>
JC> MOLECULE MISSING! Use resetpsf to start over.
JC>
JC> MOLECULE MISSING! Use resetpsf to start over.
JC>
JC> temp
JC>
JC> MOLECULE MISSING! Use resetpsf to start over.
JC>
JC> MOLECULE MISSING! Use resetpsf to start over.
JC> Couldn't open psf file temp.psf
JC> ERROR) Could not read file temp.psf
JC> Unable to load structure file temp.psf
JC> extra characters after close-quote
JC> can't read "lseg": no such variable
JC> can't read "selover": no such variable
JC> can't read "resover": no such variable
JC> invalid command name "}"
JC>
JC> MOLECULE MISSING! Use resetpsf to start over.
JC>
JC> MOLECULE MISSING! Use resetpsf to start over.
JC> Info) VMD for LINUX, version 1.8.6 (April 6, 2007)
JC> Info) Exiting normally.
JC>
JC>
JC> Do you have any suggestion?
JC>
JC> Best wishes
JC> Jose Correa
JC>
JC> --
JC>

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
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