VMD-L Mailing List

From: jouko_at_uchicago.edu
Date: Thu Jul 08 2010 - 22:21:25 CDT

I am trying to make a pdb and psf for 1 DPPC molecule from
PALM, PCGL, and the EST1 and EST2 patches, but vmd gives me
error messages. I am including the script which
I used to generate the pdb, and the error messages that follow.

package require psfgen
topology top_all27_prot_lipid.rtf
segment plm1 {pdb palm1.pdb; first none; last none}
segment plm2 {pdb palm2.pdb; first none; last none}
segment pcgl {pdb pcgl.pdb; first none; last none}
coordpdb palm1.pdb plm1
coordpdb palm2.pdb plm2
coordpdb pcgl.pdb pcgl
patch EST1 plm1:1 pcgl:1
patch EST2 plm2:1 pcgl:1
guesscoord
regenerate angles dihedrals
writepdb dppc.pdb
writepsf dppc.psf
exit

Info) VMD for LINUX, version 1.8.6 (April 6, 2007)
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) Multithreading available, 8 CPUs detected.
Info) Free system memory: 2820MB (71%)
1.4.5
reading topology file top_all27_prot_lipid.rtf

> CHARMM22 All-Hydrogen Topology File for Proteins and Lipids <<
>>>>>> Includes phi, psi cross term map (CMAP) correction <<<<<<
>>>>>>>>>>>>>>>>>>>>>> July 2004 <<<<<<<<<<<<<<<<<<<<<<<<<<
 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
building segment PLM1
reading residues from pdb file palm1.pdb
extracted 1 residues from pdb file
setting patch for first residue to NONE
setting patch for last residue to NONE
Info: generating structure...
Info: segment complete.
building segment PLM2
reading residues from pdb file palm2.pdb
extracted 1 residues from pdb file
setting patch for first residue to NONE
setting patch for last residue to NONE
Info: generating structure...
Info: segment complete.
building segment PCGL
reading residues from pdb file pcgl.pdb
extracted 1 residues from pdb file
setting patch for first residue to NONE
setting patch for last residue to NONE
Info: generating structure...
Info: segment complete.
reading coordinates from pdb file palm1.pdb for segment plm1
reading coordinates from pdb file palm2.pdb for segment plm2
reading coordinates from pdb file pcgl.pdb for segment pcgl
Warning: failed to set coordinate for atom H11 PCGL:1 PCGL
Warning: failed to set coordinate for atom H12 PCGL:1 PCGL
Warning: failed to set coordinate for atom H21 PCGL:1 PCGL
Warning: failed to set coordinate for atom H22 PCGL:1 PCGL
Warning: failed to set coordinate for atom H23 PCGL:1 PCGL
Warning: failed to set coordinate for atom H31 PCGL:1 PCGL
Warning: failed to set coordinate for atom H32 PCGL:1 PCGL
Warning: failed to set coordinate for atom H33 PCGL:1 PCGL
Warning: failed to set coordinate for atom H41 PCGL:1 PCGL
Warning: failed to set coordinate for atom H42 PCGL:1 PCGL
Warning: failed to set coordinate for atom H43 PCGL:1 PCGL
Warning: failed to set coordinate for atom H51 PCGL:1 PCGL
Warning: failed to set coordinate for atom H52 PCGL:1 PCGL
Warning: failed to set coordinate for atom O3 PCGL:1 PCGL
Warning: failed to set coordinate for atom O4 PCGL:1 PCGL
Warning: failed to set coordinate for atom CG1 PCGL:1 PCGL
Warning: failed to set coordinate for atom HG11 PCGL:1 PCGL
Warning: failed to set coordinate for atom HG12 PCGL:1 PCGL
Warning: failed to set coordinate for atom CG2 PCGL:1 PCGL
Warning: failed to set coordinate for atom HG21 PCGL:1 PCGL
Warning: failed to set coordinate for atom OG2 PCGL:1 PCGL
Warning: failed to set coordinate for atom HO2 PCGL:1 PCGL
Warning: failed to set coordinate for atom CG3 PCGL:1 PCGL
Warning: failed to set coordinate for atom HG31 PCGL:1 PCGL
Warning: failed to set coordinate for atom HG32 PCGL:1 PCGL
Warning: failed to set coordinate for atom OG3 PCGL:1 PCGL
Warning: failed to set coordinate for atom HO3 PCGL:1 PCGL
applying patch EST1 to 2 residues
applying patch EST2 to 2 residues
Info: guessing coordinates for 30 atoms (7 non-hydrogen)
Warning: poorly guessed coordinates for 27 atoms (7 non-hydrogen):
Warning: poorly guessed coordinate for atom H2A PCGL:1 PCGL
Warning: poorly guessed coordinate for atom C6 PCGL:1 PCGL
Warning: poorly guessed coordinate for atom C7 PCGL:1 PCGL
Warning: poorly guessed coordinate for atom C8 PCGL:1 PCGL
Warning: poorly guessed coordinate for atom H5A PCGL:1 PCGL
Warning: poorly guessed coordinate for atom H5B PCGL:1 PCGL
Warning: poorly guessed coordinate for atom H6A PCGL:1 PCGL
Warning: poorly guessed coordinate for atom H6B PCGL:1 PCGL
Warning: poorly guessed coordinate for atom H6C PCGL:1 PCGL
Warning: poorly guessed coordinate for atom H7A PCGL:1 PCGL
Warning: poorly guessed coordinate for atom H7B PCGL:1 PCGL
Warning: poorly guessed coordinate for atom H7C PCGL:1 PCGL
Warning: poorly guessed coordinate for atom H8A PCGL:1 PCGL
Warning: poorly guessed coordinate for atom H8B PCGL:1 PCGL
Warning: poorly guessed coordinate for atom H8C PCGL:1 PCGL
Warning: poorly guessed coordinate for atom H4A PCGL:1 PCGL
Warning: poorly guessed coordinate for atom H4B PCGL:1 PCGL
Warning: poorly guessed coordinate for atom OP3 PCGL:1 PCGL
Warning: poorly guessed coordinate for atom OP4 PCGL:1 PCGL
Warning: poorly guessed coordinate for atom OP1 PCGL:1 PCGL
Warning: poorly guessed coordinate for atom OP2 PCGL:1 PCGL
Warning: poorly guessed coordinate for atom H3A PCGL:1 PCGL
Warning: poorly guessed coordinate for atom H3B PCGL:1 PCGL
Warning: poorly guessed coordinate for atom H1A PCGL:1 PCGL
Warning: poorly guessed coordinate for atom H1B PCGL:1 PCGL
Warning: poorly guessed coordinate for atom H1 PCGL:1 PCGL
Warning: failed to guess coordinates for 4 atoms
regenerating all angles
regenerating all dihedrals
Info: writing pdb file parm/dppc.pdb
Info: Atoms with guessed coordinates will have occupancy of 0.0.
Info: pdb file complete.
Info: writing psf file parm/dppc.psf
total of 136 atoms
total of 131 bonds
total of 257 angles
total of 353 dihedrals
total of 4 impropers
total of 0 cross-terms
Info: psf file complete.
PLM1:1 PCGL:1
PLM2:1 PCGL:1
Info) VMD for LINUX, version 1.8.6 (April 6, 2007)
Info) Exiting normally.
vmd >

Thanks,

Jouko