VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Mar 16 2016 - 11:25:51 CDT

Hi,
  Perhaps I'm missing something, but VMD does read and process the
PDB "CONECT" records when they are present, but this only works when
the atom count is less than 99,999, as per the spec:
  http://www.bmsc.washington.edu/CrystaLinks/man/pdb/part_69.html

I should also note that the PDB CONECT records are intended only for
"special" bonds, e.g. disulfide, that would not normally be guessed
by simple distance-based heuristics.

If your structure comes from the PDB, you could try using the "autopsf"
plugin in VMD to have it try and complete the structure (and bonds) for you.

Cheers,
  John

On Wed, Mar 16, 2016 at 10:56:34AM +0100, Norman Geist wrote:
> If VMD doesn't get any bond information from any input file, it will guess
> bonds for visualization purpose. This guessing is done based on elements
> vdw radii but before the elements are guessed from atom names, if also
> this information is not available. If you have overlapping polymers which
> VMD should not show to be bonded, you need to tell VMD where to draw the
> bonds. This can be done from the TCL interface or by passing a suitable
> parameter file, which describes your system e.g. prmtop or psf.
> Unfortunately VMD doesn't care about either the connectivity table in PDB
> files nor the TER lines.
>
>
>
> Norman Geist
>
>
>
> Von: ABHISHEK GUPTA [mailto:akgiitm_at_gmail.com]
> Gesendet: Mittwoch, 16. Maerz 2016 08:35
> An: Norman Geist <norman.geist_at_uni-greifswald.de>
> Betreff: Re: vmd-l: Unable to visualize my polymer chains generated using
> RIS theory using VMD properly
>
>
>
> What do you mean by saying "Proper bond information" ?
>
> KIndly clarify
>
> I was giving the bond connectivity information at the lower of the PDB
> file to show the connectivity.
>
> Is this problem due to steric hindrance of the non-bonded atoms in
> polyethylene chain ? Does VMD chose some distance criterion to connect
> atoms ?
>
> Regards
>
> Abhishek
>
>
>
> On Tue, Mar 15, 2016 at 1:23 PM, Norman Geist
> <[1]norman.geist_at_uni-greifswald.de> wrote:
>
> If the atoms are that close, you won't get any reasonable bond guessing
> at all. You may want to supply a parameter file to VMD which contains
> the proper bond information.
>
>
>
>
>
> Norman Geist
>
>
>
> Von: [2]owner-vmd-l_at_ks.uiuc.edu [mailto:[3]owner-vmd-l_at_ks.uiuc.edu] Im
> Auftrag von ABHISHEK GUPTA
> Gesendet: Samstag, 12. Maerz 2016 04:10
> An: [4]vmd-l_at_ks.uiuc.edu
> Betreff: vmd-l: Unable to visualize my polymer chains generated using
> RIS theory using VMD properly
>
>
>
> Hello,
>
> I am trying to visualize the simple polyethylene chains (multiple
> chains) consisting of certain number of atoms generated using RIS theory
> using VMD. I'm using the PDB format to express coordinates to visualize
> my chains. The chains are very random and at some points multiple atoms
> of a chain comes very near to each other. Sometimes, even there is inter
> chain overlapping and multiple atoms of different chains comes in close
> vicinity of each other. In such a situation, while visualizing via. VMD,
> there appears a bond between those close or very close atoms within a
> chain or between two chains. Therefore, the visulaization by VMD shows
> that number of bonds is much greater than the number of atoms and forms
> a cage like structure (in some cases) between the closely spaced or
> overlapping atoms. What might be the possible cause of this ? Does VMD
> connects Atoms taking in some distance criterion ? Can we change that
> distance criteria that VMD utilize to connect the atoms of a polymer
> chain in succession ?
>
> Thanks and Regards
>
> Abhishek Kumar Gupta
>
>
>
> References
>
> Visible links
> 1. mailto:norman.geist_at_uni-greifswald.de
> 2. mailto:owner-vmd-l_at_ks.uiuc.edu
> 3. mailto:owner-vmd-l_at_ks.uiuc.edu
> 4. mailto:vmd-l_at_ks.uiuc.edu 

-- 
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