VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Jun 20 2011 - 15:34:01 CDT

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
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