From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Tue Jun 24 2008 - 21:18:33 CDT
If you look at the terms that were actually skipped (eg, in the topology
file), you'll note that they have definitions involving atoms from the
previous or next residue, and thus shouldn't be used at all (the
topology definitions for residues include these bonds/impropers/cmap
terms for the middle of the chain, but they're just discarded at the
appropriate termini).
Peter
haosheng_at_hec.utah.edu wrote:
> 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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