VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Tue Sep 05 2006 - 10:53:35 CDT

hi,

plese check out the manual or search the mailing list archive
before asking questions like this one. if you type:

Warning: poorly guessed coordinate site:ks.uiuc.edu

into google you'll easily get about 80 hits, e.g.:

http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/6662.html

cheers,
   axel.

On 9/5/06, Lechuga, Javier <j.lechuga_at_cranfield.ac.uk> wrote:
> 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
>
> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
  Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.