VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jun 21 2011 - 09:10:16 CDT

Jianing,
  VMD will either use the radii data from the files you load, or in absence
of this information, it will do its best to guess the radii from lookup tables
according to atomic element and/or atom name fields. If you are using the
radii for Delphi calculations and VMD was forced to "guess" your radii,
due to lack of information in your original input files, then I think
you should consider using the pdb2pqr server/software to compute the
radii instead of using VMD's guess, just to be on the safe side.

Cheers,
  John Stone
  johns_at_ks.uiuc.edu

On Tue, Jun 21, 2011 at 11:00:33AM +0800, jnsong wrote:
> Dear John,
>
> Thank you very much for your reply!
>
> I just load my psf and pdb file into VMD, and then use 'save coordinate'
> and file type 'pqr', and I get radius in my new generated pdb file.
>
> Could you please tell me the accuracy of the radius produced by vmd?
> Could I use these radius in Delphi to get binding free energy?
>
> Thanks!
>
> Jianing
>
>
>
>
>
>
>
>
> On Mon, 2011-06-20 at 15:34 -0500, John Stone wrote:
> > Hi,
> > For the purposes of generating a small number of PQR files,
> > it is probably much simpler to use VMD, as VMD can do things like
> > guess the atomic radii, where catdcd doesn't know how to do this.
> >
> > Chers,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> > On Sat, Jun 18, 2011 at 02:25:15PM +0800, jnsong wrote:
> > > Dear all,
> > >
> > > I want to use catdcd to generate qpr format file. and the command is
> > > ----------------------------------------------------------------------
> > > catdcd -o 120.pqr -otype pqr -stype psf -s ribumd.psf -first 1 -last 5
> > > -dcd ribu_eq_120.dcd
> > > ----------------------------------------------------------------------
> > >
> > > ribumd.psf is my psf file and ribu_eq_120.dcd is my dcd file.
> > >
> > > But I got the following Warning:
> > > ----------------------------------------------------------------------
> > > CatDCD 4.0
> > > Opening file '120.pqr' for writing.
> > > pqrplugin) Warning no atom radii available, assigning radii of 1.0
> > > dcdplugin) detected standard 32-bit DCD file of native endianness
> > > dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later)
> > > Opened file 'ribu_eq_120.dcd' for reading.
> > > Read 5 frames from file ribu_eq_120.dcd, wrote 5.
> > > Total frames: 5
> > > Frames written: 5
> > > CatDCD exited normally.
> > > -----------------------------------------------------------------------
> > >
> > > In my file of 120.pqr, the radius of all atom is 1.0.
> > >
> > > Do I have to provide addtional file that contain radius of all atom? If
> > > so, how can I do this? What command line should I give to catdcd?
> > >
> > > Thank you very much!
> > >
> > > Jianing
> > >
> > >
> > > --
> > > Jianing Song
> > > Ph. D. Student
> > > Institute of Theoretical and Computational Sciences
> > > Dept. Phys.
> > > East China Normal University
> > > 200062
> > > 3663 North Zhongshan Road
> > > Shanghai, P. R. China
> >
> 

-- 
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