VMD-L Mailing List

From: Lin (lavizgal_at_yahoo.com.sg)
Date: Fri Mar 24 2006 - 08:29:01 CST

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!?
Yahoo! Movies - Search movie info and celeb profiles 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