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

psfgen) >>>>> Includes phi, psi cross term map (CMAP) correction <<<<<<< psfgen) >>>>>>>>>>>>>>>>>>>>>> December, 2003 <<<<<<<<<<<<<<<<<<<<<<<<<< psfgen) All comments to ADM jr. via the CHARMM web site: www.charmm.org

psfgen)

psfgen) psfgen) Created by CHARMM version 31 1 psfgen) cross-term entries present in topology definitions psfgen) reading topology file toppar_all22_prot_heme.str

parameter set discussion forum

psfgen) Topology and Parameter Stream File for heme and related psfgen) ligands and patches. psfgen) psfgen) reading topology from stream file psfgen) Topology for heme and related compounds and patches psfgen) psfgen) Created by CHARMM version 31 1 psfgen) skipping parameters in stream file psfgen) additional parameters for heme psfgen) Note: majority of heme parameters are in the protein psfgen) parameter file psfgen) psfgen) aliasing residue HIS to HSE psfgen) aliasing residue ILE atom CD1 to CD psfgen) aliasing residue MSE to MET psfgen) aliasing residue MET atom SE to SD psfgen) aliasing residue HEM to HEME psfgen) aliasing residue CYH to CYS LMP LMC CWT psfgen) building segment LMP psfgen) reading residues from pdb file LMP.pdb psfgen) unknown residue type K 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) 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) 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) 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) 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) 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) 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) 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) 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) 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) 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) 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)

failed! ERROR: failed on end of segment MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.

unknown residue type K

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$