VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Nov 22 2006 - 12:12:14 CST

Hi,
  You can safely ignore the bond errors that VMD is emitting as they
will go away if you load the PSF file first, and the PDB file second.
I would however recommend that you switch to VMD 1.8.5, as the version
you are using is a pre-release test version of VMD and not an
official release. You will find that doing the same operations on VMD 1.8.5
should be a little smoother due to the larger maximum per-atom bond counts
and other changes in the new versions of the program.

  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Nov 21, 2006 at 10:06:50PM +0100, annalisa_at_biotec.tu-dresden.de wrote:
> Hi all,
> I am trying to run a simulation of rhodopsin in membrane.
> After building the membrane and inserting the protein into the membrane
> I saved both coordinates of membrane and protein.
> When I run the combine.tcl script I get the following error messages in
> the log file (my suspicion is that this has something to do with vmd
> version that I use, that is vmd 1.8.4):
>
> Info) VMD for LINUX, version 1.8.4a22 (October 11, 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) Multithreading available, 2 CPUs detected.
> on
> 1.4.3
> reading topology file /home/bioinf/annalisa/Rhodopsin_simul/top27rodlip.inp
>
> >>>>>> Combined CHARMM All-Hydrogen Topology File for <<<<<<<<<
> >>>>>>>>> CHARMM22 Proteins and CHARMM27 Lipids <<<<<<<<<<
> from
> >>>>>>>>CHARMM22 All-Hydrogen Topology File for Proteins <<<<<<
> >>>>>>>>>>>>>>>>>>>>> August 1999 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<
> >>>>>>> Direct comments to Alexander D. MacKerell Jr. <<<<<<<<<
> >>>>>> 410-706-7442 or email: alex,mmiris.ab.umd.edu <<<<<<<<<
> and
> \\\\\\\ CHARMM27 All-Hydrogen Lipid Topology File ///////
> \\\\\\\\\\\\\\\\\\ Developmental /////////////////////////
> Alexander D. MacKerell Jr.
> August 1999
> All comments to ADM jr. email: alex,mmiris.ab.umd.edu
> telephone: 410-706-7442
>
> Created by CHARMM version 27 1
> *ERROR! Explicit exclustions not supported, atom ignored.
> ERROR! Explicit exclustions not supported, atom ignored.*
> reading topology file /home/bioinf/annalisa/Rhodopsin_simul/retinal_top.inp
>
> Created by CHARMM version 22 1
> reading structure from psf file
> /home/bioinf/annalisa/Rhodopsin_simul/membrane.psf
>
> reading coordinates from pdb file
> /home/bioinf/annalisa/Rhodopsin_simul/membrane.pdb
> reading structure from psf file
> /home/bioinf/annalisa/Rhodopsin_simul/1u19_new.psf
>
> reading coordinates from pdb file
> /home/bioinf/annalisa/Rhodopsin_simul/1u19_new_new.pdb
>
> temp
> Info: writing psf file temp.psf
> total of 43415 atoms
> total of 40516 bonds
> total of 68271 angles
> total of 92122 dihedrals
> total of 2112 impropers
> Info: psf file complete.
> Info: writing pdb file temp.pdb
> Info: pdb file complete.
> Info) Using plugin pdb for structure file temp.pdb
> Info) Using plugin pdb for coordinates from file temp.pdb
> Info) Determining bond structure from distance search ...
> *ERROR) MolAtom 32514: Exceeded maximum number of bonds (8).
> ERROR) MolAtom 10278: Exceeded maximum number of bonds (8).
> ERROR) MolAtom 5363: Exceeded maximum number of bonds (8).
> ERROR) MolAtom 42101: Exceeded maximum number of bonds (8).
> ERROR) MolAtom 6837: Exceeded maximum number of bonds (8).
> ERROR) MolAtom 40429: Exceeded maximum number of bonds (8).
> ERROR) MolAtom 18336: Exceeded maximum number of bonds (8).
> ERROR) MolAtom 40723: Exceeded maximum number of bonds (8).
> ERROR) MolAtom 35120: Exceeded maximum number of bonds (8).
> ERROR) MolAtom 40723: Exceeded maximum number of bonds (8).
> ERROR) MolAtom 19808: Exceeded maximum number of bonds (8).
> ERROR) MolAtom 19806: Exceeded maximum number of bonds (8).
> ERROR) MolAtom 18336: Exceeded maximum number of bonds (8).
> ERROR) MolAtom 6165: Exceeded maximum number of bonds (8).
> ERROR) MolAtom 7003: Exceeded maximum number of bonds (8).
> ERROR) MolAtom 19956: Exceeded maximum number of bonds (8).
> ERROR) MolAtom 19177: Exceeded maximum number of bonds (8).
> ERROR) MolAtom 20747: Exceeded maximum number of bonds (8).
> ERROR) MolAtom 5497: Exceeded maximum number of bonds (8).
> ERROR) MolAtom 6300: Exceeded maximum number of bonds (8).
> ERROR) MolAtom 33660: Exceeded maximum number of bonds (8).
> ERROR) MolAtom 19270: Exceeded maximum number of bonds (8).
> ERROR) MolAtom 39303: Exceeded maximum number of bonds (8).
> ERROR) MolAtom 20361: Exceeded maximum number of bonds (8).
> ERROR) MolAtom 7523: Exceeded maximum number of bonds (8).
> ERROR) BaseMolecule: Excessive bonding errors encountered, perhaps atom
> coordinates are in the wrong units?
> ERROR) BaseMolecule: Silencing bonding error messages.*
> Info) Finished with coordinate file temp.pdb.
> Info) Analyzing structure ...
> Info) Atoms: 43415
> Info) Bonds: 56999
> Info) Residues: 4070
> Info) Waters: 2893
> *ERROR) Residue exceeded maximum number of bonds (4).
> ERROR) Residue exceeded maximum number of bonds (4).
> ERROR) Residue exceeded maximum number of bonds (4).
> ERROR) Residue exceeded maximum number of bonds (4).
> ERROR) Residue exceeded maximum number of bonds (4).
> ERROR) Residue exceeded maximum number of bonds (4).
> ERROR) Residue exceeded maximum number of bonds (4).
> ERROR) Residue exceeded maximum number of bonds (4).
> *
>
>
>
> I have no clue how to handle these errors. Any suggestion or help is
> really appreciated!!
> Thanks
> Annalisa
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078