vmd-l: Generating PSF for 1JNO.pdb chain A

From: Lin (lavizgal_at_yahoo.com.sg)
Date: Fri Apr 14 2006 - 10:29:07 CDT

> > Hi all,
> >
> > I have problems building the PSF for chain A of
> > 1jNO.pdb.
> > However, i have missing residues...how do i include
> the
> > parameters for unknown residues?? Or do u all know
> wat
> > is
> > the problem with the following:
> >
> >
> > duplicate residue key STEA will be ignored
> > duplicate residue key PCGL will be ignored
> > duplicate residue key EST1 will be ignored
> > duplicate residue key EST2 will be ignored
> > aliasing residue DLE to LEU
> > aliasing residue DVA to VAL
> > aliasing residue ETA atom O to OG
> > building segment GA1
> > setting patch for first residue to NONE
> > setting patch for last residue to NONE
> > reading residues from pdb file chainA.pdb
> > unknown residue type FOR
> > unknown residue type ETA
> > extracted 17 residues from pdb file
> > Info: generating structure...
> > unknown residue type FOR
> >
> >
> -------------------------------------------------------
> >
> > thank you!!
> >
> >
> >
> > __________________________________
> > Do you Yahoo!?
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> > and photos.
> > http://sg.movies.yahoo.com/> # STEP 1: Build Protein
> >
> >
> > # Select chain A and chain B
> > # set chainA [atomselect top "chain A and not
> > hydrogen"]
> >
> > # Write these atoms to separate pdb files
> > #$chainA writepdb chainA.pdb
> >
> >
> > # Script to build the protein structure of GA
> > # Run with "psfgen < >
> > package require psfgen
> >
> > # Use the specified CHARMM27 topology file.
> > topology top_all27_prot_lipid.inp
> >
> > # D-Leucine and D-Valine have the same topology as
> the
> > # usual L-Leu and L-Val residues, they're just mirror
> > # images. Hence we can use the existing topology
> file.
> > # We also pdbalias an atom in the ethanolamide
> residue
> > so
> > # that psfgen doesn't have to guess the position of
> the
> > atom.
> > pdbalias residue DLE LEU
> > pdbalias residue DVA VAL
> > pdbalias atom ETA O OG
> >
> > # Build two segments, one for each chain.
> > segment GA1 {
> > first NONE
> > last NONE
> > pdb chainA.pdb
> > }
> >
> >
> >
> > # Load the coordinates for each segment.
> > coordpdb chainA.pdb GA1
> >
> >
> > # Write out the psf file
> > writepsf chainA.psf
> >
> > # Guess the positions of missing atoms. As long as
> all
> > the heavy
> > # atoms are present, psfgen usually does a very good
> > job of this.
> > guesscoord
> > writepdb chainA.pdb
> >
> > mol load psf chainA.psf pdb chainA.pdb
> >
> >
>
>
>
>
> __________________________________
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> > # STEP 1: Build Protein
>
>
> # Select chain A and chain B
> # set chainA [atomselect top "chain A and not
> hydrogen"]
>
> # Write these atoms to separate pdb files
> #$chainA writepdb chainA.pdb
>
>
> # Script to build the protein structure of GA
> # Run with "psfgen < >
> package require psfgen
>
> # Use the specified CHARMM27 topology file.
> topology top_all27_prot_lipid.inp
>
> # D-Leucine and D-Valine have the same topology as the
> # usual L-Leu and L-Val residues, they're just mirror
> # images. Hence we can use the existing topology file.
> # We also pdbalias an atom in the ethanolamide residue
> so
> # that psfgen doesn't have to guess the position of the
> atom.
> pdbalias residue DLE LEU
> pdbalias residue DVA VAL
> pdbalias atom ETA O OG
>
> # Build two segments, one for each chain.
> segment GA1 {
> first NONE
> last NONE
> pdb chainA.pdb
> }
>
>
>
> # Load the coordinates for each segment.
> coordpdb chainA.pdb GA1
>
>
> # Write out the psf file
> writepsf chainA.psf
>
> # Guess the positions of missing atoms. As long as all
> the heavy
> # atoms are present, psfgen usually does a very good
> job of this.
> guesscoord
> writepdb chainA.pdb
>
> mol load psf chainA.psf pdb chainA.pdb
>
>

                
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