Problem regarding psfgen

From: haosheng_at_hec.utah.edu
Date: Tue Jun 24 2008 - 18:03:08 CDT

I met a problem when I'm trying to generate psf file for a protein.
These "skipping..." Info actually destroy the starting, turning and
ending part of the protein while keeps the other part well. I have
tried two similiar structures (one have one chain the other has two),
both return the same Info line. Here are my psfgen and the error lines:

#########################psfgen#################################
package require psfgen
topology top_all27_prot_lipid.inp

rm -f 1ZWW_protein.pdb 1ZWW_water.pdb 1ZWW_protein_A.pdb 1ZWW_protein_B.pdb
rm NBAR.pdb NBAR.psf

pdbalias residue HOH TIP3
pdbalias residue HIS HSD
pdbalias atom ILE CD1 CD

grep -v HETATM 1ZWW.pdb > 1ZWW_protein.pdb
grep HETATM 1ZWW.pdb > 1ZWW_water.pdb

grep " A " 1ZWW_protein.pdb > 1ZWW_protein_A.pdb
grep " B " 1ZWW_protein.pdb > 1ZWW_protein_B.pdb

segment A {
pdb 1ZWW_protein_A.pdb
}
coordpdb 1ZWW_protein_A.pdb A

segment B {
pdb 1ZWW_protein_B.pdb
}
coordpdb 1ZWW_protein_B.pdb B

writepdb NBAR.pdb
writepsf NBAR.psf
exit

#####################################################################
Created by CHARMM version 31 1
cross-term entries present in topology definitions
aliasing residue HOH to TIP3
aliasing residue HIS to HSD
aliasing residue ILE atom CD1 to CD
building segment A
reading residues from pdb file 1X03_protein.pdb
extracted 202 residues from pdb file
Info: generating structure...
Info: skipping improper N-C-CA-HN at beginning of segment.
Info: skipping cross-term C-N-CA-C-N-CA-C-N at beginning of segment.
Info: skipping conformation C-N-CA-C at beginning of segment.
Info: skipping conformation C-CA-N-HN at beginning of segment.
Info: skipping bond C-N at end of segment.
Info: skipping improper C-CA-N-O at end of segment.
Info: skipping cross-term C-N-CA-C-N-CA-C-N at end of segment.
Info: skipping conformation CA-C-N-CA at end of segment.
Info: skipping conformation N-CA-C-O at end of segment.
Info: skipping conformation N-CA-C-N at end of segment.
A:26
A:247
Info: segment complete.
reading coordinates from pdb file 1X03_protein.pdb for segment A
Warning: failed to set coordinate for atom O ALA:247 A
Warning: failed to set coordinate for atom OXT ALA:247 A
Info: writing pdb file NBAR.pdb
Info: pdb file complete.
Info: writing psf file NBAR.psf
total of 3274 atoms
total of 3295 bonds
total of 5988 angles
total of 8766 dihedrals
total of 565 impropers
total of 200 cross-terms
Info: psf file complete.
Info) VMD for LINUX, version 1.8.6 (April 6, 2007)
Info) Exiting normally.

Thank you in advance,
Haosheng

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