Dear All,
I have run several simulations. But, I need to analyse a selective number
of structures from each simulation saved at a given time step "t". Thus,
for a 20ns simulation, starting t=0 and incrementing it by 50ps, I'll have
~400 individual structures. Each structure is within a waterbox, which
contains approx. 20,000 water molecules. Once I get the structures, I need
to do the following using CHIMERA:
1. Open each structure and save water molecules within a cutoff distance of
5.0 Angstrom from the protein. Thus, I'll end-up having a shell (<=5.0A)
of water molecules around the protein. The saved structure will be in
.pdb format and include the protein with 5.0A water shell.
I know how to do it in CHIMERA using the commandline option/pulldown
menu, but, how to do it for 400 structures. Is there a way to run it
in a "Batch Job" ?
2. I also need to superimpose Ca-Ca atoms of 400 structures. But, I feel
there is a limit to the no. of structures that CHIMERA could handle,
thus, at max. I would be superimposing 20-30 structures at a time. How
could I automatize the same through a script sothat I could run it in
batches?
Thanks in advance. Any suggestion(s) is welcomed.
Warm regards,
Tuhin
