The easiest option is catDCD I guess, it supports also many other formats. An usage example would look like:

catdcd -otype dcd -o my.dcd -crdbox my1.crd -crdbox my2.crd

As you can see, you can also simply concatenate trajectories that way. The tool is now shipped with VMD but you can also dowload it at:

http://www.ks.uiuc.edu/Development/MDTools/catdcd/

Converting trajectory frames of different MD codes to each other is not recommended since you face with many forcefield and topology errors as using them. Why do you want to convert it to NAMD trj.?

I have to perform covariance and network analysis on my proteins. If I'm not wrong, R accepts only .dcd files as input and not .crd. That's the whole point of converting the file formats.

Try using VMD Tk console; Load the Amber trj. frames together with the parameters file (.parm).

animate dup frame $frame 0

incr frame

animate goto $frame

animate write dcd $dcd-file beg 0 end $frame waitfor all

The first solution that came in my mind is maybe you can use VMD to change the format by loading your molecule on VMD and then save the new format :

1.load your molecule and trajectory

2. select your molecule

3. VMD > File > save coordinates

u can use the mdconvert (mdtraj)

in addition to mdtraj cpptraj can also do it:

$cpptraj

parm system.prmtop

trajin system.rst

trajout system.dcd

go

Hi,

Can any one suggest me to convert -out.cms or desmond based trj files to .dcd file?

Hi,

Are you still working on Amber?