From: gurunath katagi (gurukatagi_at_gmail.com)
Date: Sun Apr 12 2009 - 19:43:48 CDT
> Hello sir,
> >>I wanted to create psf file for hemoglobin molecule (tetramer) (pdbid :
> 4HHB)
> I want to include all the HETATM in the psf file expect water molecules.
> I have written a script which is as explained in the NAMD manual.
>
> When I run the script , psf file is generated, but when the molecule is
> loaded, the heme moeities does't show up.
>
> Please suggest me any modification to the script or describe the steps
that
> i have to take for psf file creation for this molecule.
>
> I am attatching the file for you refernce.
> 4HHB.pdb -- pdb file for which i have to create the psf file.
> file.tcl --- script to create the chains.
> after this I manually deleted the HEM and HOH molecules from this.
> psfffile.tcl -- for creation of the file.
> hemoglobin.pdb -- pdb file creted after the script is run
> hemoglobin.psf -- psf file created.
>
> >>in the tutorail , when you do ,
> set ubq [atomslelect top protein]
> $protein writepdb ubqp.pdb -- ubqp.pdb file is creted in which all
> HETATM are deleted.
>
> but when you do,..
> set chainA [atomslelect top "chain A"]
> $chainA writepdb chainA.pdb ----- chainA.pdb file is creted in which
> HETATM have been conevrted to ATOM and all HEM ad HOH are retained.
> this is in contrast with the prevous example in which these have been
> deleted.
>
> Why does this happen or am i making a mistake?
>
> >> how do we get to know about the alias for the atom and residues to be
> used.
> eg: PO4 and HEME ...etc
>
> Please reply
>
> thank you
> with Regrads
>
> Gurunath
>
> -
> Gurunath M Katagi
> M.Sc (engg) Research student
> Supercomputer Education and Research Centre
> Indian Institute Of Science
> Bangalore
-- NIH Resource for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801 Email: johns_at_ks.uiuc.edu Phone: 217-244-3349 WWW: http://www.ks.uiuc.edu/~johns/ <http://www.ks.uiuc.edu/%7Ejohns/> Fax: 217-244-6078 -- Gurunath M Katagi M.Sc (engg) Research student Supercomputer Education and Research Centre Indian Institute Of Science Bangalore
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