VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Aug 29 2007 - 00:08:39 CDT

Hi,
  There are a number of variations to the DCD format, depending
on what program emits the file, what word size and
endianism the host machine is, and whether or not certain options
are enabled or in-use. The DCD plugin HTML text and older DCD
I/O code (such as old code snippets) are far behind where the current
generation of the VMD plugin has evolved. Can you tell me what
CHARMM or simulaid say when you attempt to load the DCD file?
It is possible there's a bug in the VMD DCD writing code that only
crops up on 64-bit platforms, but I was not previously aware of any,
so I'll need much more information. Can you send me a copy of the DCD
file in question by uploading it to the VMD Public project on Biocore?:
  http://www.ks.uiuc.edu/Research/vmd/alpha/

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Aug 28, 2007 at 06:50:52PM -0400, dimka wrote:
> Hello!
>
> I'm having trouble having my VMD-generated trajectories (Linux, AMD64)
> not read by other programs like charmm or simulaid. (is anybody else
> having the same problem?)
>
> Can anybody point me to a fortran routine that reads VMD-generated dcd
> files? If not maybe there's a where there are exact
> specifications/format to vmd-written DCD files. So far I've found
> only this two links that seem to conflict:
> http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/dcdplugin.html
> and a c routine sent by JS in this thread:
> http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/5305.html
>
> According the dcdplugin.html, NTITLE is integer*2 (FORTRAN), while the
> C code defines 'int NTITLE;'
>
> is integer*2 in FORTRAN is the same as 'int NTITLE' in C? 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078