missing atoms warnings for psfgen

From: Frances Leung (frances_leung_at_rogers.com)
Date: Mon Jan 19 2004 - 21:47:33 CST

Hello,
 
I'm working on a protein complex that has a large number of residues
missing from the PDB file to begin with, when I was creating the psf
structure file, I got a lot of warnings regarding missing atoms at the
end of segment. Is this normal? Does the guesscoord command take care
of adding back in all of the atoms? What should I do about the missing
residues? The log file for generated the psf file is attached. The psf
file was generated using the following script.
 
 
 
topology parameters/top_all22_prot.inp
 
alias residue HIS HSD
 
# (2) Build protein segment and read coordinates
segment seg0 {
 pdb myfile_frag0.pdb
}
coordpdb myfile_frag0.pdb seg0
 
segment seg1 {
 pdb myfile_frag1.pdb
}
coordpdb myfile_frag1.pdb seg1
 
segment seg2 {
 pdb myfile_frag2.pdb
}
coordpdb myfile_frag2.pdb seg2
 
segment seg3 {
 pdb myfile_frag3.pdb
}
coordpdb myfile_frag3.pdb seg3
 
segment seg4 {
 pdb myfile_frag4.pdb
}
coordpdb myfile_frag4.pdb seg4
 
segment seg5 {
 pdb myfile_frag5.pdb
}
coordpdb myfile_frag5.pdb seg5
 
segment seg6 {
 pdb myfile_frag6.pdb
}
coordpdb myfile_frag6.pdb seg6
 
segment seg7 {
 pdb myfile_frag7.pdb
}
coordpdb myfile_frag7.pdb seg7
 
 
# (3) Guess missing coordinates
guesscoord
 
# (4) Write structure and coordinate files
writepsf output_psf/1i7x_psfgen_psf.psf
writepdb output_psf/1i7x_psfgen_pdb.pdb
 
 
Frances
 
 


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