VMD-L Mailing List

From: ABHISHEK GUPTA (akgiitm_at_gmail.com)
Date: Sat Mar 19 2016 - 00:06:59 CDT

Thankyou Norman & John,

As you told me to build a psf file in VMD for clearly seeing only the
bonded atoms without showing bonds between unbonded atoms,
I have tried to build a psf file for my PDB from a code in VMD site but the
code that converts the CONECT info in VMD to PSF file is given in binary
and i couldn't understand how to use it.
Can you please answer how to create a psf file for my PDB coordinate file
for polyetylene chains so that i will be able to visualize my structure
properly
without bonding between the unbonded atoms ?

Thanks and Regards

On Wed, Mar 16, 2016 at 9:55 PM, John Stone <johns_at_ks.uiuc.edu> wrote:

> 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
>
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/
>