Tutorial-l Mailing List

From: Sujata Sovani (sujatas_at_scripps.edu)
Date: Tue Jul 28 2009 - 18:01:18 CDT

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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