VMD-L Mailing List

From: Lechuga, Javier (j.lechuga_at_cranfield.ac.uk)
Date: Tue Sep 05 2006 - 10:23:35 CDT

Hello,
 
Using psfGen I am getting the result bellow. I wonder if that is ok anyway.
 
<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
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
extracted 216 residues from pdb file
Info: generating structure...
Info: segment complete.
reading coordinates from pdb file DPPC1.pdb for segment U
regenerating all angles
regenerating all dihedrals
Info: guessing coordinates for 288 atoms (144 non-hydrogen)
Warning: poorly guessed coordinates for 288 atoms (144 non-hydrogen):
Warning: poorly guessed coordinate for atom O2 PALM:1 U
Warning: poorly guessed coordinate for atom H2 PCGL:2 U
Warning: poorly guessed coordinate for atom H1 PCGL:2 U
Warning: poorly guessed coordinate for atom O2 PALM:3 U
Warning: poorly guessed coordinate for atom O2 PALM:4 U
Warning: poorly guessed coordinate for atom H2 PCGL:5 U
Warning: poorly guessed coordinate for atom H1 PCGL:5 U
Warning: poorly guessed coordinate for atom O2 PALM:6 U
Warning: poorly guessed coordinate for atom O2 PALM:7 U
Warning: poorly guessed coordinate for atom H2 PCGL:8 U
Warning: poorly guessed coordinate for atom H1 PCGL:8 U
Warning: poorly guessed coordinate for atom O2 PALM:9 U
Warning: poorly guessed coordinate for atom O2 PALM:10 U
Warning: poorly guessed coordinate for atom H2 PCGL:11 U
Warning: poorly guessed coordinate for atom H1 PCGL:11 U
Warning: poorly guessed coordinate for atom O2 PALM:12 U
Warning: poorly guessed coordinate for atom O2 PALM:13 U
Warning: poorly guessed coordinate for atom H2 PCGL:14 U
Warning: poorly guessed coordinate for atom H1 PCGL:14 U
Warning: poorly guessed coordinate for atom O2 PALM:214 U
...
Warning: poorly guessed coordinate for atom H2 PCGL:215 U
Warning: poorly guessed coordinate for atom H1 PCGL:215 U
Warning: poorly guessed coordinate for atom O2 PALM:216 U
Info: writing pdb file DPPC\DPPC36A.pdb
Info: Atoms with guessed coordinates will have occupancy of 0.0.
Info: pdb file complete.
Info: writing psf file DPPC\DPPC36A.psf
total of 9648 atoms
total of 9432 bonds
total of 18000 angles
total of 24840 dihedrals
total of 144 impropers
Info: psf file complete.
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.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 
Thankyou