Re: [AMBER] analyzing DESMOND MD trajectories in cpptraj...

From: Jason Swails <jason.swails.gmail.com>
Date: Thu, 20 Dec 2012 14:11:04 -0700

Try creating a PDB file from the maestro topology file instead. PDB files can be used in place of amber topologies in cpptraj.

HTH,
Jason

--
Jason M. Swails
Quantum Theory Project
University of Florida
Ph.D. Candidate
352-392-4032
On Dec 20, 2012, at 12:01 PM, Shashidhar Rao <shashidharr.gmail.com> wrote:
> Dear CPPTRAJ Gurus,
> 
> I am attempting to analyze DESMOND MD trajectories in cpptraj.  Toward this
> end, I used VMD to convert the DESMOND MD trajectories to DCD formatted
> files.  However, when I tried to read one such file in cpptraj using the
> command
> 
> trajin a.dcd
> 
> I obtained a console message indicating that "Could not get Parameter
> file".  I was wondering if I need to use VMD to convert the maestro CMS
> file to the amber parm file???
> 
> any suggestions would be very helpful and appreciated.
> 
> Shashi Rao
> 
> -- 
> Shashidhar N. Rao
> 3 SERINA DRIVE
> PLAINSBORO
> NEW JERSEY 08536 USA
> 
> shashidharr.gmail.com
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Received on Thu Dec 20 2012 - 13:30:02 PST