Subject: generating polypeptide oligos with X-PLOR; Re: CCL:Dear SIRS

From: root <[email-masked]>
Date: Fri, 6 Mar 1998 14:58:24 +0300 (MSK)

Dear CCLers,

On Fri, 6 Mar 1998, Renate Griffith wrote:
> [...] The mindset that can not even conceive of scientists being other
> than male (as in "Dear Sirs, ...) is extremely hurtful. Quite apart from
> being wrong. [...]

I think this would give us a fascinating opportunity to conduct an
informal poll -- what is the percentile of nonmales in the computational
chemistry field? While certainly being multiply biased, this would at
least supply ballpark figures. If nobody else will, I volunteer to count
the voices. 

To make this post somewhat less off-topic: relatively recently I've asked
the list about methods to generate pdb and psf files for polypeptide
oligos. To complete the mini-summary I already provided: Andrew Atkinson
via bionet.software.x-plor kindly supplied the following solution: first
generate a psf file e.g. with the following X-PLOR script (polylys50mer): 

topology @TOPPAR:topallhdg.pro end

segment
   name="BLAH"
   chain
      link pept head - * tail + * end
      first nter  tail + * end
      last ctn head - * end
      sequence
        LYS LYS LYS LYS LYS LYS LYS LYS LYS LYS
        LYS LYS LYS LYS LYS LYS LYS LYS LYS LYS
        LYS LYS LYS LYS LYS LYS LYS LYS LYS LYS
        LYS LYS LYS LYS LYS LYS LYS LYS LYS LYS
        LYS LYS LYS LYS LYS LYS LYS LYS LYS LYS
      end
   end
end

write structure output=polylysine.psf end
stop

And feed the shiny new .psf blob into the the script coming with the
X-PLOR tutorial (tutorial/nmr/generate_template.inp). The resulting pdb
structure is steepest descent minimized and already subjected to some MD
relaxation.

Helmut Grubmueller's Solvate can handle the resulting structure. However,
when using salt water for solvating matrix, it inserts references to
toph19.nacl into the generated mkpsf.inp X-PLOR script. This parameter
file is is not part of Solvate nor comes with X-PLOR nor is visible by
AltaVista. As Helmut is currently on the move -- does anybody have a
pointer to toph19.nacl? 

Polylysine made thusly is totally ionized, and lacks counterions.  While
counterions should be easy to add, estimating the dissociation coefficient
of a protein polyelectrolyte appears difficult. I understand forcefields
used in biochemistry do not allow for bond breakage/formation as e.g. MM2
is purported to be able to do, so a polyelectrolyte must enter the MD
arena sensibly dissociated. Apart from extracting these data from an
experiment, e.g. via electrophoretic mobility, is there a sofware package
capable of predicting peptide polyelectrolyte dissociation coefficients
under roughly physiological conditions? 

Regards,
Eugene Leitl