From: Olya Kravchenko (okrav_at_ucdavis.edu)
Date: Fri May 14 2004 - 19:46:26 CDT
Hi all! I am trying to make psf file that consist of many segments. When I try
to make psf for either one of the segments I have the following error:
"duplicate segment key" and then "failed on segment". Here is what I have in
*.log file:
Created by CHARMM version 27 1
duplicate residue key CO will be ignored
aliasing residue ILE atom CD1 to CD
aliasing residue HIS to HSE
building segment APRO
setting patch for first residue to NTER
setting patch for last residue to CTER
reading residues from pdb file chainA.pdb
extracted 514 residues from pdb file
Info: generating structure...
Info: skipping improper N-C-CA-HN 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 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.
Info: segment complete.
applying patch TYHI to 2 residues
reading coordinates from pdb file chainA.pdb for segment APRO
building segment APRO
duplicate segment key APRO
ERROR: failed on segment
MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.
reading coordinates from pdb file chainA.pdb for segment APRO
Warning: failed to set coordinate for atom N MET:1 APRO
Warning: failed to set coordinate for atom CA MET:1 APRO
Warning: failed to set coordinate for atom C MET:1 APRO
etcetera...
Here is my entry in the *.pgn file for that segment:
package require psfgen
topology my_topology.inp
alias atom ILE CD1 CD
alias residue HIS HSE
segment APRO {
first NTER
last CTER
pdb chainA.pdb
}
patch TYHI APRO:244 APRO:240
coordpdb chainA.pdb APRO
guesscoord
writepdb oxidase.pdb
writepsf oxidase.psf
I've already done the same procedure with practically identical molecule,
except for that coordinates were shifted in z direction, with the same
topology file and identical pgn. The format of pdb file is also exactly the
same as in my previous run. Has anyone encountered something like that
before? Please, help!
Thanks in advance,
Olga
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