VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Aug 20 2012 - 10:44:50 CDT

Hi,
  I don't know anything about using Packmol, but if there's a way to label
the chain components by modifying one of the PDB files like the B-factor
column, that might help you get what you want. So long as the numbers
make it into VMD, you could then select by the values in the columns that
you modified. You may want to talk to the Packmol authors about that.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Aug 17, 2012 at 07:21:59PM +0000, simao.pereira_at_di3.units.it wrote:
> Hi John,
>
> Indeed I could have given more details.
> Thanks for your suggestion, in fact the atoms in each chains are sequentially numbered and this works very well.
>
> I came across another solution that consist in deleting the nanoparticle core and saving the system in a new
> file. When loaded the new file, VMD distinguished the chains by fragments and that could also do the trick.
>
> I am facing another issue now.
> I am packing the grafted nanoparticle in a box with polymer chains using packmol. As input, I use two pdb files (polymer.pdb and nanoparticle.pdb).
> I also got the corresponding .psf files using the pdfgen. How can I introduce the topology of the polymer chains and nanoparticle in the output file of packmol (a single .pdb file)?
>
> Best,
> Simão
>
> -----Original Message-----
> From: John Stone [mailto:johns_at_ks.uiuc.edu]
> Sent: 17 August 2012 17:24
> To: Pereira Simao
> Cc: vmd-l_at_ks.uiuc.edu
> Subject: Re: vmd-l: select grafted chains in nanoparticle
>
> Hi,
> You didn't say anything about whether these individual chains are tagged in some way in the structure files (e.g. with different chain names, or some other tag you could use to identify them)? What about the range of atom indices? If the atoms in each of those changes are in a strictly consecutive sequence. For convenience you could you could make atom selection macros that map some easy to type thing like "part1"
> to index range selections like "index 739 to 9467".
>
> Cheers,
> John
>
> On Thu, Aug 16, 2012 at 04:04:47PM +0000, simao.pereira_at_di3.units.it wrote:
> > Hi all,
> >
> >
> >
> > I have a system with a nanoparticle and several chains grafted onto it. I
> > would like to do some measurements on each chain (for instance radii of
> > gyration).
> >
> > The issue is that there is no straight way to select each individual chain
> > (as far as I know).
> >
> > Is there a way to select each chain, starting from the atom at the
> > grafting point until the end of the chain?
> >
> > I thought about selecting atoms by their connectivity but since chains are
> > long (100 CRU) that may be a bit cumbersome.
> >
> > Any (good) suggestion is welcome :)
> >
> >
> >
> > Best,
> >
> >
> >
> > Simao Pereira
> >
> >
> >
> > P.S.: I have been using Materials Studio to create the initial system and
> > LAMMPS to carry out the dynamics.
> >
> >
> >
> > #############################################
> >
> > PhD Student
> >
> > DI3 - University of Trieste
> >
> > Via Valerio 10 - 34127 Trieste (Italy)
> >
> > Mobile +39 3201860285
> >
> > Email: simao.pereira_at_di3.units.it
> >
> > #############################################
> >
> >
>
> --
> NIH Resource 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/ Fax: 217-244-6078
>
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-- 
NIH Resource 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/       Fax: 217-244-6078