Generating psf for NPC1

From: Joshua Lioi (jlioi_at_nd.edu)
Date: Thu Nov 19 2009 - 10:45:07 CST

I'm new to namd and working with proteins, and I could use some help. I'm
trying to use psfgen to get a psf for the protein NPC1 (pdb here:
http://www.pdb.org/pdb/explore/explore.do?structureId=3GKH) in order to do
molecular dynamics simulations with it. I'm having some issues, which I know
are at least partly due to GOL and NAG ligands. Can anyone give me some help
to get this psf in working order? I made a pgn script using the psf
tutorial and I've attached that and my input files. The output from running
the program is as follows. I'm removing repetitious warnings and replacing
them with ellipses. Thanks for any help you can give.

duplicate type key H
.
duplicate type key NS2
duplicate residue key ALA will be ignored
.
duplicate residue key EST2 will be ignored
aliasing residue HIS to HSE
aliasing residue ILE atom CD1 to CD
building segment 3GKH
reading residues from pdb file in_files/3GKH_protein.pdb
extracted 225 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.
Info: segment complete.
applying patch DISU to 2 residues
applying patch DISU to 2 residues
applying patch DISU to 2 residues
applying patch DISU to 2 residues
applying patch DISU to 2 residues
applying patch DISU to 2 residues
applying patch DISU to 2 residues
applying patch DISU to 2 residues
applying patch DISU to 2 residues
reading coordinates from pdb file in_files/3GKH_protein.pdb for segment 3GKH
Warning: failed to set coordinate for atom O CYS:247 3GKH
aliasing residue HOH to TIP3
building segment SOLV
disabling angle autogeneration
disabling dihedral autogeneration
reading residues from pdb file in_files/3GKH_water.pdb

unknown residue type NAG
unknown residue type NAG
unknown residue type NAG
unknown residue type GOL
unknown residue type GOL
extracted 100 residues from pdb file
Info: generating structure...
unknown residue type NAG
ERROR: failed on end of segment
MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.

 - Josh Lioi


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