VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Fri Feb 27 2009 - 22:01:19 CST

On Fri, 27 Feb 2009, Nikolay Simakov wrote:

NS> Thanks Alex,
NS>
NS>
NS> I do pretty much nothing with pdb just load whatever gromacs gives me.
NS>
NS> Here is how system looks
NS> http://crete.chem.cmu.edu/~mikola/ch1/ch2.png
NS> And here is pdb file:
NS> http://crete.chem.cmu.edu/~mikola/ch1/ch2.pdb
NS>
NS> Funny thing is that windows version eats it without problem,

and all the vmd versions (current cvs, self-compiled; 1.8.7a48;
1.8.7a33) that i have access to, work without a problem, too.

do you by any chance use native language support (aka NLS)?

can you try running vmd after an

export LC_ALL=C

(or in case you are on csh diet: setenv LC_ALL C )

and check whether it makes a difference?

that is about the only thing that i could imagine
that would be messing with the parsing (it can change
how sscanf recognizes numbers).

cheers,
   axel.

NS>
NS> Nick
NS>
NS> Axel Kohlmeyer wrote:
NS> > On Fri, 27 Feb 2009, Nikolay Simakov wrote:
NS> >
NS> > nikolay,
NS> >
NS> > NS> Thank you John for reply,
NS> > NS>
NS> > NS> I understand that VMD utilize simple distance method, still it should
NS> > NS> work
NS> > NS> in my case.
NS> >
NS> > depends. how standard conformant is your pdb file?
NS> > how do you generate the partial files? with a text editor?
NS> >
NS> > parsing non-standard conforming pdb file can give quite surprising
NS> > results.
NS> >
NS> > can you upload the files somewhere (e.g. VMD biocore project), where they
NS> > can be inspected more closely and we can track down,
NS> > what they do to the pdb parser in the VMD's file reader library?
NS> >
NS> > thanks,
NS> > axel.
NS> >
NS> > NS> I have install 1.8.7 with the same results. What is more interesting I
NS> > NS> have
NS> > NS> try vmd 1.8.6 on windows machine and its give me perfect results. I
NS> > NS> also
NS> > NS> have try different newline code and it still doesn't give me anything
NS> > NS> positive.
NS> > NS>
NS> > NS> Nikolay
NS> > NS>
NS> > NS> John Stone wrote:
NS> > NS> > Nick,
NS> > NS> > VMD uses a simple distance-based bond search heuristic which can
NS> > NS> > make mistakes in some cases. I'd suggest that you try using one of
NS> > NS> > the new test versions of VMD 1.8.7 (rather than an older version)
NS> > NS> > and
NS> > NS> > let us know if you still have trouble. If you do, then you might
NS> > NS> > see
NS> > NS> > if running the autopsf plugin on your structure will assign correct
NS> > NS> > bonds even when the model is in a single molecule.
NS> > NS> >
NS> > NS> > Cheers,
NS> > NS> > John Stone
NS> > NS> > vmd_at_ks.uiuc.edu
NS> > NS> >
NS> > NS> > On Fri, Feb 27, 2009 at 05:01:30PM -0500, Nikolay Simakov wrote:
NS> > NS> >
NS> > NS> > > Hi,
NS> > NS> > >
NS> > NS> > > I have next problem. Then I load pdb file which has protein and
NS> > NS> > > lipids,
NS> > NS> > > vmd create bonds between protein and lipids and do not create
NS> > NS> > > bonds
NS> > NS> > > withing lipids. If I split protein and lipids into separate pdb
NS> > NS> > > files
NS> > NS> > > and then load them separately everything is fine.
NS> > NS> > >
NS> > NS> > > I am running vmd-1.8.6 under linux. I also try to downgrade and
NS> > NS> > > check is
NS> > NS> > > it working or not and found that 1.7.1 is doing good.
NS> > NS> > >
NS> > NS> > > Has anyone have similar problems?
NS> > NS> > >
NS> > NS> > > Nick
NS> > NS> > >
NS> > NS> >
NS> > NS> >
NS> > NS>
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.