Using PsfGen

From: Lechuga, Javier (j.lechuga_at_cranfield.ac.uk)
Date: Mon Aug 28 2006 - 14:29:52 CDT

Hello,
 
Found a pdb file for a DPPC lipid, however, when I try to generate the Psf file using "top_all27_lipid.rtf" into PsfGen, I get the following:
 
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
Found 44 plugins or data handlers in directory

'C:/Program Files/University of Illinois/VMD/plugins/WIN32/molfile'.

1.3.4

reading topology file top_all27_lipid.rtf

\\\\\\\ CHARMM27 All-Hydrogen Lipid Topology File ///////

\\\\\\\\\\\\\\\\\\ Developmental /////////////////////////

Alexander D. MacKerell Jr.

December, 2003

All comments to ADM jr. via the CHARMM web site: www.charmm.org

parameter set discussion forum

Created by CHARMM version 27 1

building segment U

reading residues from pdb file DPPC1.pdb

unknown residue type MOL

extracted 1 residues from pdb file

Info: generating structure...

unknown residue type MOL

ERROR: failed on end of segment

MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.

reading coordinates from pdb file DPPC1.pdb for segment U

Warning: failed to set coordinate for atom P MOL:1 U

Warning: failed to set coordinate for atom N MOL:1 U

Warning: failed to set coordinate for atom O MOL:1 U

Warning: failed to set coordinate for atom O1 MOL:1 U

Warning: failed to set coordinate for atom O2 MOL:1 U

Warning: failed to set coordinate for atom O3 MOL:1 U

Warning: failed to set coordinate for atom C MOL:1 U

Warning: failed to set coordinate for atom C1 MOL:1 U

Warning: failed to set coordinate for atom C2 MOL:1 U

Warning: failed to set coordinate for atom C3 MOL:1 U

Warning: failed to set coordinate for atom C4 MOL:1 U

Warning: failed to set coordinate for atom O4 MOL:1 U

Warning: failed to set coordinate for atom O5 MOL:1 U

Warning: failed to set coordinate for atom C5 MOL:1 U

Warning: failed to set coordinate for atom C6 MOL:1 U

Warning: failed to set coordinate for atom C7 MOL:1 U

Warning: failed to set coordinate for atom C8 MOL:1 U

Warning: failed to set coordinate for atom C9 MOL:1 U

Warning: failed to set coordinate for atom C10 MOL:1 U

Warning: failed to set coordinate for atom C11 MOL:1 U

Warning: failed to set coordinate for atom C12 MOL:1 U

Warning: failed to set coordinate for atom C13 MOL:1 U

Warning: failed to set coordinate for atom C14 MOL:1 U

Warning: failed to set coordinate for atom C15 MOL:1 U

Warning: failed to set coordinate for atom C16 MOL:1 U

Warning: failed to set coordinate for atom O6 MOL:1 U

Warning: failed to set coordinate for atom O7 MOL:1 U

Warning: failed to set coordinate for atom C17 MOL:1 U

Warning: failed to set coordinate for atom C18 MOL:1 U

Warning: failed to set coordinate for atom C19 MOL:1 U

Warning: failed to set coordinate for atom C20 MOL:1 U

Warning: failed to set coordinate for atom C21 MOL:1 U

Warning: failed to set coordinate for atom C22 MOL:1 U

Warning: failed to set coordinate for atom C23 MOL:1 U

Warning: failed to set coordinate for atom C24 MOL:1 U

Warning: failed to set coordinate for atom C25 MOL:1 U

Warning: failed to set coordinate for atom C26 MOL:1 U

Warning: failed to set coordinate for atom C27 MOL:1 U

Warning: failed to set coordinate for atom C28 MOL:1 U

Warning: failed to set coordinate for atom H5 MOL:1 U

Warning: failed to set coordinate for atom H6 MOL:1 U

Warning: failed to set coordinate for atom H3 MOL:1 U

Warning: failed to set coordinate for atom H4 MOL:1 U

Warning: failed to set coordinate for atom H7 MOL:1 U

Warning: failed to set coordinate for atom H8 MOL:1 U

Warning: failed to set coordinate for atom H9 MOL:1 U

Warning: failed to set coordinate for atom H10 MOL:1 U

Warning: failed to set coordinate for atom 1H2 MOL:1 U

Warning: failed to set coordinate for atom 2H2 MOL:1 U

Warning: failed to set coordinate for atom 3H2 MOL:1 U

Warning: failed to set coordinate for atom 4H2 MOL:1 U

Warning: failed to set coordinate for atom 5H2 MOL:1 U

Warning: failed to set coordinate for atom 6H2 MOL:1 U

Warning: failed to set coordinate for atom 7H2 MOL:1 U

Warning: failed to set coordinate for atom 8H2 MOL:1 U

Warning: failed to set coordinate for atom H29 MOL:1 U

Warning: failed to set coordinate for atom H30 MOL:1 U

Warning: failed to set coordinate for atom H31 MOL:1 U

Warning: failed to set coordinate for atom H32 MOL:1 U

Warning: failed to set coordinate for atom H33 MOL:1 U

Warning: failed to set coordinate for atom H34 MOL:1 U

Warning: failed to set coordinate for atom H1 MOL:1 U

Warning: failed to set coordinate for atom H11 MOL:1 U

Warning: failed to set coordinate for atom H12 MOL:1 U

Warning: failed to set coordinate for atom H13 MOL:1 U

Warning: failed to set coordinate for atom H14 MOL:1 U

Warning: failed to set coordinate for atom H15 MOL:1 U

Warning: failed to set coordinate for atom H16 MOL:1 U

Warning: failed to set coordinate for atom H17 MOL:1 U

Warning: failed to set coordinate for atom H18 MOL:1 U

Warning: failed to set coordinate for atom H19 MOL:1 U

Warning: failed to set coordinate for atom H20 MOL:1 U

Warning: failed to set coordinate for atom H2 MOL:1 U

Warning: failed to set coordinate for atom C1 METH:1 U

Warning: failed to set coordinate for atom 1H1 METH:1 U

Warning: failed to set coordinate for atom 2H1 METH:1 U

Warning: failed to set coordinate for atom C1 METH:1 U

Warning: failed to set coordinate for atom 1H1 METH:1 U

Warning: failed to set coordinate for atom 2H1 METH:1 U

Warning: failed to set coordinate for atom C1 METH:1 U

Warning: failed to set coordinate for atom 1H1 METH:1 U

Warning: failed to set coordinate for atom 2H1 METH:1 U

Warning: failed to set coordinate for atom C1 METH:1 U

Warning: failed to set coordinate for atom 1H1 METH:1 U

Warning: failed to set coordinate for atom 2H1 METH:1 U

Warning: failed to set coordinate for atom C1 METH:1 U

Warning: failed to set coordinate for atom 1H1 METH:1 U

Warning: failed to set coordinate for atom 2H1 METH:1 U

Warning: failed to set coordinate for atom C1 METH:1 U

Warning: failed to set coordinate for atom 1H1 METH:1 U

Warning: failed to set coordinate for atom 2H1 METH:1 U

Warning: failed to set coordinate for atom 3H1 METH:1 U

Warning: failed to set coordinate for atom C1 METH:1 U

Warning: failed to set coordinate for atom 1H1 METH:1 U

Warning: failed to set coordinate for atom 2H1 METH:1 U

Warning: failed to set coordinate for atom C1 METH:1 U

Warning: failed to set coordinate for atom 1H1 METH:1 U

Warning: failed to set coordinate for atom 2H1 METH:1 U

Warning: failed to set coordinate for atom 3H1 METH:1 U

Warning: failed to set coordinate for atom C1 METH:1 U

Warning: failed to set coordinate for atom 1H1 METH:1 U

Warning: failed to set coordinate for atom 2H1 METH:1 U

Warning: failed to set coordinate for atom 3H1 METH:1 U

Warning: failed to set coordinate for atom C1 METH:1 U

Warning: failed to set coordinate for atom 1H1 METH:1 U

Warning: failed to set coordinate for atom 2H1 METH:1 U

Warning: failed to set coordinate for atom 3H1 METH:1 U

Warning: failed to set coordinate for atom C1 METH:1 U

Warning: failed to set coordinate for atom 1H1 METH:1 U

Warning: failed to set coordinate for atom 2H1 METH:1 U

Warning: failed to set coordinate for atom 3H1 METH:1 U

ERROR: failed on guessing coordinates

Info: writing pdb file DPPC\DPPC.pdb

ERROR: failed on writing coordinates to pdb file

Info: writing psf file DPPC\DPPC.psf

ERROR: failed on writing structure to psf file

vmd > Info) VMD for WIN32, version 1.8.3 (February 15, 2005)

Info) http://www.ks.uiuc.edu/Research/vmd/

Info) Email questions and bug reports to vmd_at_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) No joysticks found. Joystick interface disabled.

Info) VMD for WIN32, version 1.8.3 (February 15, 2005)

Info) Exiting normally.

>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>

Thank you

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