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bd-macbook-pro:building_LmP-LmCytc briandinhnguyen$ vmd -dispdev text -e psfgen.tcl


Info) VMD for MACOSXX86, version 1.9.1 (February 4, 2012)
Info) http://www.ks.uiuc.edu/Research/vmd/
Info) Email questions and bug reports to vmd@ks.uiuc.edu
Info) Please include this reference in published work using VMD:
Info)
Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
Info)
Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
Info) ------------------------------------------------------------Info) Multithreading available, 4 CPUs detected.
Info) Dynamically loaded 2 plugins in directory:
Info) /Applications/VMD 1.9.1.app/Contents/vmd/plugins/MACOSXX86/molfile
LMP-LMC-COMPLEX
1.6
psfgen) reading topology file top_all22_prot_pCAM-FES.inp
psfgen)
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LMP LMC
CWT
psfgen)
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psfgen)

>>>>>>>>CHARMM22 All-Hydrogen Topology File for Proteins <<<<<<


>>>>> Includes phi, psi cross term map (CMAP) correction <<<<<<<
>>>>>>>>>>>>>>>>>>>>>> December, 2003 <<<<<<<<<<<<<<<<<<<<<<<<<<
All comments to ADM jr. via the CHARMM web site: www.charmm.org
parameter set discussion forum
Created by CHARMM version 31 1
cross-term entries present in topology definitions
reading topology file toppar_all22_prot_heme.str
Topology and Parameter Stream File for heme and related
ligands and patches.
reading topology from stream file
Topology for heme and related compounds and patches
Created by CHARMM version 31 1
skipping parameters in stream file
additional parameters for heme
Note: majority of heme parameters are in the protein
parameter file
aliasing
aliasing
aliasing
aliasing
aliasing
aliasing

residue
residue
residue
residue
residue
residue

HIS
ILE
MSE
MET
HEM
CYH

to HSE
atom CD1 to CD
to MET
atom SE to SD
to HEME
to CYS

building segment LMP


reading residues from pdb file LMP.pdb
unknown residue type K
unknown residue type HOH
unknown residue type HOH
unknown residue type HOH
unknown residue type HOH
unknown residue type HOH
unknown residue type HOH
unknown residue type HOH
unknown residue type HOH
unknown residue type HOH
unknown residue type HOH
unknown residue type HOH
unknown residue type HOH
unknown residue type HOH
unknown residue type HOH
unknown residue type HOH
unknown residue type HOH
unknown residue type HOH
unknown residue type HOH
unknown residue type HOH
unknown residue type HOH
unknown residue type HOH

psfgen)
psfgen)
psfgen)
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psfgen)
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psfgen)

unknown
unknown
unknown
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unknown

residue
residue
residue
residue
residue
residue
residue
residue
residue
residue
residue
residue
residue
residue
residue
residue
residue
residue
residue
residue
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residue
residue
residue
residue
residue
residue
residue
residue
residue
residue
residue
residue
residue
residue
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residue
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residue
residue
residue
residue
residue
residue
residue
residue
residue
residue
residue
residue
residue
residue
residue
residue
residue
residue
residue

type
type
type
type
type
type
type
type
type
type
type
type
type
type
type
type
type
type
type
type
type
type
type
type
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type
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type
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type
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type
type
type
type
type
type
type
type
type
type
type
type
type
type
type
type
type
type
type
type
type
type
type

HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH

psfgen)
psfgen)
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psfgen)

unknown
unknown
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unknown

residue
residue
residue
residue
residue
residue
residue
residue
residue
residue
residue
residue
residue
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residue
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residue
residue
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residue
residue
residue
residue
residue
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residue
residue
residue
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residue
residue
residue
residue
residue
residue

type
type
type
type
type
type
type
type
type
type
type
type
type
type
type
type
type
type
type
type
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type
type
type
type
type
type
type
type
type
type
type
type
type
type
type
type
type
type
type
type
type

HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH
HOH

psfgen) unknown residue type HOH


psfgen) unknown residue type HOH
psfgen) unknown residue type HOH
psfgen) unknown residue type HOH
psfgen) unknown residue type HOH
psfgen) unknown residue type HOH
psfgen) unknown residue type HOH
psfgen) unknown residue type HOH
psfgen) unknown residue type HOH
psfgen) unknown residue type HOH
psfgen) unknown residue type HOH
psfgen) unknown residue type HOH
psfgen) unknown residue type HOH
psfgen) unknown residue type HOH
psfgen) unknown residue type HOH
psfgen) extracted 447 residues from pdb file
psfgen) Info: generating structure...psfgen) unknown residue type K
failed!
ERROR: failed on end of segment
MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.
MOLECULE MISSING!

Use resetpsf to start over.

MOLECULE MISSING!

Use resetpsf to start over.

MOLECULE MISSING!

Use resetpsf to start over.

MOLECULE MISSING!

Use resetpsf to start over.

MOLECULE MISSING!

Use resetpsf to start over.

MOLECULE MISSING! Use resetpsf to start over.


Info) VMD for MACOSXX86, version 1.9.1 (February 4, 2012)
Info) Exiting normally.
vmd > bd-macbook-pro:building_LmP-LmCytc briandinhnguyen$