VMD-L Mailing List

From: Chitrak Gupta (chgupta_at_mix.wvu.edu)
Date: Sun Mar 20 2016 - 17:27:42 CDT

Hi Abhishek,

Look through the "Generating a Protein Structure File (PSF)" section of the
NAMD tutorial (VMD also has a automatic PSF generator, but I am slightly
old-fashioned in this, I still use the script). I am assuming you already
have topology files for your system. With that and the PDB file, you should
be able to generate a PSF file and view the molecule in VMD.

Hope this helps,
Chitrak.

On Sat, Mar 19, 2016 at 1:06 AM, ABHISHEK GUPTA <akgiitm_at_gmail.com> wrote:

> 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/
>>
>
>