From: Cesar Luis Avila (cavila_at_fbqf.unt.edu.ar)
Date: Mon Aug 28 2006 - 15:23:05 CDT
I think there might be several problems with your system.
1) The lipid is named MOL in the pdb. It should be named DPPC, or at
least create an alias for this residue.
2) DPPC is not defined on CHARMM topology. Nevertheless the groups
needed to build the topology do exist. So you should edit the topology
file.
3) You should also check that the atoms name in the pdb file match those
used on the topology file.
Regards
Cesar Avila
Lechuga, Javier escribió:
> 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/usr/local/lib/vmd/plugins/noarch/tcl/readcharmmtop1.0/top_all27_prot_lipid_na.inp
>
>
> 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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