RE: NAMD: HEM residue

From: Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Wed May 04 2005 - 15:17:34 CDT

Could you provide us your input file, please?
Cheers,
Michel

-----Original Message-----
From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On
Behalf Of surendra negi
Sent: Wednesday, May 04, 2005 2:57 PM
To: namd-l_at_ks.uiuc.edu
Subject: namd-l: NAMD: HEM residue

Hi All,
 I am trying to create a psf file from PDB. My PDB
file has both HOH and HEM entry. The script I wrote is
running file till HOH. But it is unable to guess
coordinate for HEM. Here is the log file generated by
NAMD. Thanks a lot for help or suggestions.
Regards
surendra
----------LOG FILE-------
reading residues from pdb file output/test_protein.pdb
extracted 465 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.
*** writing psf structure file ***
Info: writing psf file output/test.psf
total of 7479 atoms
total of 7573 bonds
total of 13693 angles
total of 20147 dihedrals
total of 1218 impropers
Info: psf file complete.

*** guessing missing coordinates ***
Info: guessing coordinates for 3748 atoms (2
non-hydrogen)
Warning: poorly guessed coordinates for 5 atoms (2
non-hydrogen):
Warning: poorly guessed coordinate for atom HT1
GLY:28 XPRT
Warning: poorly guessed coordinate for atom HT2
GLY:28 XPRT
Warning: poorly guessed coordinate for atom HT3
GLY:28 XPRT
Warning: poorly guessed coordinate for atom OT1
HSE:492 XPRT
Warning: poorly guessed coordinate for atom OT2
HSE:492 XPRT
*** writing pdb coordinate file ***
Info: writing pdb file output/test.pdb
Info: Atoms with guessed coordinates will have
occupancy of 0.0.
Info: pdb file complete.
*** advanced demo begins here ***
*** adding a segment of water ***
aliasing residue HOH to TIP3
building segment SOLV
disabling angle autogeneration
disabling dihedral autogeneration
reading residues from pdb file output/test_water.pdb
extracted 261 residues from pdb file
Info: generating structure...
Info: segment complete.
*** reading water coordinates ***
aliasing residue HOH atom O to OH2

*** guessing missing coordinates ***
Info: guessing coordinates for 3748 atoms (2
non-hydrogen)
Warning: poorly guessed coordinates for 5 atoms (2
non-hydrogen):
Warning: poorly guessed coordinate for atom HT1
GLY:28 XPRT
Warning: poorly guessed coordinate for atom HT2
GLY:28 XPRT
Warning: poorly guessed coordinate for atom HT3
GLY:28 XPRT
Warning: poorly guessed coordinate for atom OT1
HSE:492 XPRT
Warning: poorly guessed coordinate for atom OT2
HSE:492 XPRT
*** writing pdb coordinate file ***
Info: writing pdb file output/test.pdb
Info: Atoms with guessed coordinates will have
occupancy of 0.0.
Info: pdb file complete.
*** advanced demo begins here ***
*** adding a segment of water ***
aliasing residue HOH to TIP3
building segment SOLV
disabling angle autogeneration
disabling dihedral autogeneration
reading residues from pdb file output/test_water.pdb
extracted 261 residues from pdb file
Info: generating structure...
Info: segment complete.
*** reading water coordinates ***
aliasing residue HOH atom O to OH2
...
...
...
Warning: failed to set coordinate for atom O1D
HEM:500 HEM
Warning: failed to set coordinate for atom O2D
HEM:500 HEM
*** guessing HEM coordinates - not possible ***
ERROR: failed on guessing coordinates

                
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