VMD-L Mailing List

From: Sanjib Chowdhury (sanjib_at_udel.edu)
Date: Fri Jan 17 2014 - 11:16:41 CST

Got it! Thanks - Sanjib

-----Original Message-----
From: John Stone [mailto:johns_at_ks.uiuc.edu]
Sent: Friday, January 17, 2014 12:06 PM
To: Sanjib Chowdhury
Cc: vmd-l_at_ks.uiuc.edu
Subject: Re: vmd-l: Bond order cut-off value

Hi,
  If you load your LAMMPS dump file in concert with a PSF, PDB, or another
file that assigns proper atom names, VMD will recognize the hydrogens and
avoid guessing extra bonds on your waters. This is what Axel was referring
to. At the moment after loading your LAMMPS dump file, your atoms are named
"1" and "2", so VMD can't do much with that...

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Jan 16, 2014 at 07:01:27PM -0500, Sanjib Chowdhury wrote:
> I didn't define any bond.
> For the same model, pdb format it ok. But problem (i.e., H-H bond in
> water
> molecule) arises when I use lammps dump file.
> I have attached both files here.
>
> Thanks,
> Sanjib
>
> -----Original Message-----
> From: John Stone [mailto:johns_at_ks.uiuc.edu]
> Sent: Thursday, January 16, 2014 6:02 PM
> To: Sanjib Chowdhury
> Cc: vmd-l_at_ks.uiuc.edu
> Subject: Re: vmd-l: Bond order cut-off value
>
> Hi,
> If the bond is defined in the structure file you loaded (e.g. PSF
> file), then VMD will draw it. To hide those bonds, you would need to
delete them.
> When showing ball-stick type representations, VMD draws the bonds
> exactly as they are defined by the structure, so you'd need to delete
> the bonds to get VMD to avoid showing them. If you loaded a file
> format that doesn't define bonds, and VMD guessed the bonds, then it
> may be an issue with the assignment of atoms types, VDW radii, and the
> default bond guessing scheme VMD uses. If you provide more
> information about your specific case, someone can undoubtably suggest ways
to get what you want.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
>
> On Thu, Jan 16, 2014 at 05:53:54PM -0500, Sanjib Chowdhury wrote:
> > Hi,
> >
> >
> >
> > When I visualize my water model in VMD using cpk or bond drawing
> method,
> > it shows bonding between H in the water
> >
> > molecule. How I can avoid this? I guess I need to change the bond
order
> > cut-off value. How can I change it in VMD?
> >
> >
> >
> > I will appreciate your suggestion.
> >
> >
> >
> > Thanks,
> >
> > Sanjib
> >
> >
>
> --
> 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/ 

--
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/