From: Francesco Pietra (
Date: Thu Nov 15 2007 - 09:50:36 CST

I started again from scratch. If you are so kind again to have a look at ...

(1) Created membrane.pdb and membrane.psf with membrane plugin.

(2) Inserted myprotein.pdb into the membrane, centered, and saved

(3) Loaded protein_aligned.pdb to VMD and created protein.psf using
Extensions...Modeling...Auto PSF Builder (choosing Amber type). This created,
inter alia, protein_aligned_autopsf_tmpfile.psf.
Sitting in the working directory:

(4) vmd -dispdev text < combine.tcl | tee combine.log

Error: could not open protein.psf.

(5) Boldly, renamed protein_aligned_autopsf_tmpfile.psf protein.psf.

(6) vmd -dispdev text < combine.tcl | tee combine.log
went to completion, through a series of warnings (see please attached

I can display the created protein_mem.pdb (also loading protein_mem.psf as a
trial), getting uniform view. Unable to distinguish the protein (which is in
the latter part of the protein_mem.pdb file).

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


--- Axel Kohlmeyer <> wrote:

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

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