VMD-L Mailing List

From: jnsong (jnsong_at_itcs.ecnu.edu.cn)
Date: Wed Jun 22 2011 - 02:22:59 CDT

Dear john,

I got it.

Thank you very much for all the help!

Jianing

On Tue, 2011-06-21 at 09:10 -0500, John Stone wrote:
> 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
> > >
> >
>