Re: Unable to generate PSF file due to an unparametrized component

From: Esteban Gabriel Vega Hissi (egvega_at_gmail.com)
Date: Tue Jul 28 2009 - 18:18:49 CDT

Hi,
I advise you Not to parametrize this new residue but to make a new modified
residue from existing residues in your toppar files. Try following this
tutorial:

http://www.ks.uiuc.edu/Training/Tutorials/science/topology/topology-html/

Hope this help

Esteban

2009/7/28 Sujata Sovani <sujatas_at_scripps.edu>

> 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.
> 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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