From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Mar 02 2009 - 11:15:27 CST

Hi,
  I loaded the PDB posted on your web site without any trouble
using both VMD 1.8.6 and VMD 1.8.7a56 (both on Linux).
I believe that your problem is related to your language/locale
settings, as Axel had already theorized. Since I can display this
structure without any trouble, it's likely that the libc stdio routines
are misbehaving as a result of internationalization settings on your
machine. (e.g. misparsing floating point numbers, or the like..)

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Feb 27, 2009 at 10:24:13PM -0500, Nikolay Simakov wrote:
> Thanks Alex,
>
>
> I do pretty much nothing with pdb just load whatever gromacs gives me.
>
> Here is how system looks
> http://crete.chem.cmu.edu/~mikola/ch1/ch2.png
> And here is pdb file:
> http://crete.chem.cmu.edu/~mikola/ch1/ch2.pdb
>
> Funny thing is that windows version eats it without problem,
>
> Nick
>
> Axel Kohlmeyer wrote:
> >On Fri, 27 Feb 2009, Nikolay Simakov wrote:
> >
> >nikolay,
> >
> >NS> Thank you John for reply,
> >NS>
> >NS> I understand that VMD utilize simple distance method, still it should
> >work
> >NS> in my case.
> >
> >depends. how standard conformant is your pdb file?
> >how do you generate the partial files? with a text editor?
> >
> >parsing non-standard conforming pdb file can give
> >quite surprising results.
> >
> >can you upload the files somewhere (e.g. VMD biocore project),
> >where they can be inspected more closely and we can track down,
> >what they do to the pdb parser in the VMD's file reader library?
> >
> >thanks,
> > axel.
> >
> >NS> I have install 1.8.7 with the same results. What is more interesting I
> >have
> >NS> try vmd 1.8.6 on windows machine and its give me perfect results. I
> >also
> >NS> have try different newline code and it still doesn't give me anything
> >NS> positive.
> >NS>
> >NS> Nikolay
> >NS>
> >NS> John Stone wrote:
> >NS> > Nick,
> >NS> > VMD uses a simple distance-based bond search heuristic which can
> >NS> > make mistakes in some cases. I'd suggest that you try using one of
> >NS> > the new test versions of VMD 1.8.7 (rather than an older version) and
> >NS> > let us know if you still have trouble. If you do, then you might see
> >NS> > if running the autopsf plugin on your structure will assign correct
> >NS> > bonds even when the model is in a single molecule.
> >NS> >
> >NS> > Cheers,
> >NS> > John Stone
> >NS> > vmd_at_ks.uiuc.edu
> >NS> >
> >NS> > On Fri, Feb 27, 2009 at 05:01:30PM -0500, Nikolay Simakov wrote:
> >NS> >
> >NS> > > Hi,
> >NS> > >
> >NS> > > I have next problem. Then I load pdb file which has protein and
> >lipids,
> >NS> > > vmd create bonds between protein and lipids and do not create bonds
> >NS> > > withing lipids. If I split protein and lipids into separate pdb
> >files
> >NS> > > and then load them separately everything is fine.
> >NS> > >
> >NS> > > I am running vmd-1.8.6 under linux. I also try to downgrade and
> >check is
> >NS> > > it working or not and found that 1.7.1 is doing good.
> >NS> > >
> >NS> > > Has anyone have similar problems?
> >NS> > >
> >NS> > > Nick
> >NS> > >
> >NS> >
> >NS> >
> >NS>
> >
> >

-- 
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