From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Thu Nov 15 2007 - 03:15:33 CST

axel:
Yes, my posting was badly organized.

combine.tcl is from http://www.ks.uiuc.edu/Research/vmd/plugins/membrane/
I do not attach it here because my subsequent managing has shown that the
problem is with protein.psf file. This is the result of not sticking to a
single house. I use Amber9 for MD, DOCK6.1 for docking, Chimera for dockprep,
and VMD for what that world is unable to do, or simply to have a better
insight. That mixture would require a better general command than I have
presently attained.

I am working with a pore protein model that it took long to be fully in order
for both Amber9 and DOCK6.1. The pdb file is absolutely standard (as far as VMD
pluging are concerned, HIS is HIE and ILE has CD1). Present work in Generalized
Born conditions is fully OK. A check with known ligands (treated with
Antechamber) is OK, both with computations and experimental work.

I tried both manual generation of the psf file according to tutorials at
http://www.ks.uiuc.edu/Research/vmd/plugins/psfgen/ and automatic generation
from VMD Extensions..Modeling...Automatic PSF Builder. Both arrived at wrong
psf. I am attaching the log from the last trial with Automatic generation (I
have renamed the generated "protein_autopsf_tmpfile.psf" "protein.psf" when the
former name failed). In both cases, "cross terms" are lacking from psf file.
Must say that Autopsf has parameterized 8 instances of HIE (15 atoms each) and
the single WAT (3 atoms) residue. The latter is for a (natural) molecule of
water within the pore.

Looking at protein_autopsf_tmpfile.pdb with Chimera, it is clear that the
procedure has removed the three "TER" records that I had set to get rid of
three 50A-long bonds (those long bonds are not revealed by VMD - at least not
in my default use of it - though they hinder dockprep workind and, in any case,
create problems to MD).

Thanks
francesco

--- Axel Kohlmeyer <akohlmey_at_cmm.chem.upenn.edu> wrote:

> francesco,
>
> which version of combine.tcl (there must be hundreds of scripts
> under that name. i have at least five on my machine) are you
> using and how, if at all, did you modify it.
>
> by not showing the script code you were using, only those people
> can help you, who know it and know which particular version you
> are using. if you want to increase your chances to get help, you
> have to help us by providing more information, even if they seem
> redundant or obvious to you. it is very hard to give advice without
> context.
>
> regards,
> axel.
>
>
> On 11/14/07, Francesco Pietra <chiendarret_at_yahoo.com> wrote:
> > I am in a silly loop, trying to merge protein and POPC membrane and
> removing
> > superimposition.
> >
> > I created a 100x100A POPC (less is not enough for my protein) and inserted
> and
> > centered the protein.
> >
> > Saved protein_aligned.pdb. fed to the working directory both scripts
> > combine.tcl and top_all27_prot_lipid.inp.
> >
> > The, at
> >
> > vmd -dispdev text < combine.tcl |tee combine.log
>
>
>
> >
> > the error was:
> >
> > There is no 'top' molecule in atom select's 'molId' (VMD 1.8.6).
> >
> > After resetpsf, I tried various (clearly faulty) selections with no
> success.
> >
> > Thanks for helping
> > francesco pietra
> >
> > Incidentally, does 10x100 cause steric clashes?
> >
> >
> >
>
____________________________________________________________________________________
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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.
>

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