VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Fri Feb 27 2009 - 20:47:32 CST

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> 

-- 
=======================================================================
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.