VMD-L Mailing List

From: jnsong (jnsong_at_itcs.ecnu.edu.cn)
Date: Mon Jun 20 2011 - 22:00:33 CDT

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
>