VMD-L Mailing List

From: jnsong (jnsong_at_itcs.ecnu.edu.cn)
Date: Sat Jun 18 2011 - 01:25:15 CDT

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