VMD-L Mailing List

From: Nikolay Simakov (nsimakov_at_andrew.cmu.edu)
Date: Fri Feb 27 2009 - 21:24:13 CST

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>
>
>