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

From: Lin (lavizgal_at_yahoo.com.sg)
Date: Mon Mar 27 2006 - 19:18:13 CST

--- Lin <lavizgal_at_yahoo.com.sg> wrote:

> Date: Fri, 24 Mar 2006 22:29:01 +0800 (CST)
> From: Lin <lavizgal_at_yahoo.com.sg>
> Subject: Re: vmd-l: Generating PSF for 1JNO.pdb chain A
> To: VMD Mailing List <vmd-l_at_ks.uiuc.edu>
>
> 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!!
>
>
>
> __________________________________
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> 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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