Tutorial-l Mailing List

From: Chris Harrison (charris5_at_gmail.com)
Date: Tue Jul 28 2009 - 20:41:03 CDT

To parameterize, begin with the parametrization tutorial:
http://www.ks.uiuc.edu/Training/Tutorials/science/forcefield-tutorial/forcefield-html/
AND
http://www.ks.uiuc.edu/Training/Tutorials/science/forcefield-tutorial/forcefield-tutorial-files.tar.gz

To convert to a plain histidine, open the pdb and delete all atoms of the
histidine EXCEPT those atoms corresponding to the protein backbone (C, O, N)
.... but first make a backup copy of the pdb file. ;) Remove the line in
the psfgen input file: "pdbalias residue HIS HIC", then rerun psfgen.
Psfgen should automatically generate the missing coordinates of the HIS
sidechain.

Chris 

--
Chris Harrison, Ph.D.
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
char_at_ks.uiuc.edu                            Voice: 217-244-1733
http://www.ks.uiuc.edu/~char               Fax: 217-244-6078
On Tue, Jul 28, 2009 at 6:01 PM, Sujata Sovani <sujatas_at_scripps.edu> wrote:
>
> Hi All,
>
> I am new to NAMD.
>
> I am following the tutorial at
> http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-win-html/namd-tutorial-win.html
> using the molecule of my interest.
>
> As per the tutorial I have created the .pgn file, but having some problems
> --
>
> I have a methylated histidine in the molecule that I am changing to HIS
> (may not be the right thing to do but thought will try). Here is my .pgn
> file  -
>
> ---------------------------------------------
> package require psfgen
> topology top_all27_prot_lipid.inp
> pdbalias residue HIS HIC
> segment U {pdb hlup.pdb}
> coordpdb hlup.pdb U
> guesscoord
> writepdb hlu.pdb
> writepsf hlu.psf
> ---------------------------------------------
>
> After running the .pgn file above - I get this error
>
> ERROR: Unable to open topology file top_all27_prot_lipid.inp
> MOLECULE DESTROYED BY FATAL ERROR!  Use resetpsf to start over.
>
> Then I tried AutoPSF. AutoPSF component chooser window says it has detected
> 1 unparametrized component,
> it says you can either load another topology file (I do not have another
> topology file)
> or delete the component or parametrized using paratool. It does generate an
> autopsf file but the charge and mass are 0.
>
> -- So can anyone please let me know how can I parametrize methyl histidine
> and/or convert it to plain histidine?
>
> Thank you very much.
>
> Best Regards,
> Sujata
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