From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Thu Nov 15 2007 - 22:47:21 CST

On Thu, 15 Nov 2007, Francesco Pietra wrote:

FP> I started again from scratch. If you are so kind again to have a look at ...
FP>
FP> (1) Created membrane.pdb and membrane.psf with membrane plugin.
FP>
FP> (2) Inserted myprotein.pdb into the membrane, centered, and saved
FP> protein_aligned.pdb.
FP>
FP> (3) Loaded protein_aligned.pdb to VMD and created protein.psf using
FP> Extensions...Modeling...Auto PSF Builder (choosing Amber type). This created,
FP> inter alia, protein_aligned_autopsf_tmpfile.psf.
FP>
FP> Sitting in the working directory:
FP>
FP> (4) vmd -dispdev text < combine.tcl | tee combine.log
FP>
FP> Error: could not open protein.psf.
FP>
FP> (5) Boldly, renamed protein_aligned_autopsf_tmpfile.psf protein.psf.

why do you keep doing this?? since you do have problems,
why don't you write an input to psfgen explicitely and
thus have a much better control over the whole process.
the primary job of autopsf is to make the job of building
psf files for well behaving systems easy, it is not a
replacement for knowing what you are doing. sorry.

[...]

FP> I wonder whether this is simply a problem of commands with VMD or, more likely
FP> from not having treated protein_aligned.pdb adequately. The protein model is
FP> constituted of a tetramer, each comprising two alpha-helixes, a pore protein,
FP> and a filter. I wonder whether I used the psfgen plugin correctly or should
FP> have made the protein_aligned.pdb into sections.

this is all well explained in the psfgen tutorial,
so i don't want to repeat this here.

cheers,
   axel.

FP>
FP> Thanks
FP> francesco
FP>
FP> --- Axel Kohlmeyer <akohlmey_at_cmm.chem.upenn.edu> wrote:
FP>
FP> > On Thu, 15 Nov 2007, Francesco Pietra wrote:
FP> >
FP> > FP> axel:
FP> > FP> Yes, my posting was badly organized.
FP> > FP>
FP> > FP> combine.tcl is from http://www.ks.uiuc.edu/Research/vmd/plugins/membrane/
FP> >
FP> > FP> I do not attach it here because my subsequent managing has shown that the
FP> > FP> problem is with protein.psf file. This is the result of not sticking to a
FP> >
FP> > i am inclined to disagree. please check the log file and you'll
FP> > see, that apart from some warnings, the major complaint and error
FP> > message is that the script cannot find the .pdb file protein_aligned.pdb
FP> > that is the correctly oriented and aligned version of protein.pdb.
FP> >
FP> > the rest are warnings and for as long as you were using the same
FP> > topology file to build those .psf files, i would assume, that they
FP> > are still usable.
FP> >
FP> > FP> single house. I use Amber9 for MD, DOCK6.1 for docking, Chimera for
FP> > FP> dockprep, and VMD for what that world is unable to do, or simply to
FP> > FP> have a better insight. That mixture would require a better general
FP> > FP> command than I have presently attained.
FP> >
FP> > this needs no comment.
FP> >
FP> > [...]
FP> >
FP> > FP> Looking at protein_autopsf_tmpfile.pdb with Chimera, it is clear that the
FP> > FP> procedure has removed the three "TER" records that I had set to get rid
FP> > of
FP> > FP> three 50A-long bonds (those long bonds are not revealed by VMD - at least
FP> > not
FP> > FP> in my default use of it - though they hinder dockprep workind and, in any
FP> > case,
FP> > FP> create problems to MD).
FP> >
FP> > that (again) is a reasoning, that does not make much sense to me.
FP> > the bonding information should be read from the .psf file. unless
FP> > there are CONECT records, there is no bonding information in a .pdb
FP> > file and what a program makes out of that is due to the logic (or
FP> > lack thereof) of that program.
FP> >
FP> > cheers,
FP> > axel.
FP> >
FP> > FP>
FP> > FP> Thanks
FP> > FP> francesco
FP> > FP>
FP> > FP>
FP> > FP>
FP> >
FP> > --
FP> > =======================================================================
FP> > Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu
FP> > Center for Molecular Modeling -- University of Pennsylvania
FP> > Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
FP> > tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
FP> > =======================================================================
FP> > If you make something idiot-proof, the universe creates a better idiot.
FP> >
FP>
FP>
FP>
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-- 
=======================================================================
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
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.