On Thu, 2014-03-20 at 16:45 +0530, Arunima Shilpi wrote:
> Dear Sir
>
> Presently I am following tutorial of protein-ligand tutorial (Estrogen-
> Raloxifene) tutorial to calculate binding energy by MMPBSA.
>
> Here in the tutorial its mentioned as following
>
> "The important files from the MD simuation for calculating the binding free
> energy using MMPBSA.py are the topology files and the mdcrd file (
> Est_Rec_top_mdcrd.tgz<http://ambermd.org/tutorials/advanced/tutorial3/py_script/files/Est_Rec_top_mdcrd.tgz>
> )"
>
> I have query as to whether we have to gzip topology files and the
> mdcrd file for
> complex into single file so that we have
> Est_Rec_top_mdcrd.tgz<http://ambermd.org/tutorials/advanced/tutorial3/py_script/files/Est_Rec_top_mdcrd.tgz>
I don't think I understand your question (or what caused the confusion).
The only reason the files are zipped and archived together in a single
compressed tarball is because it's easier to download the files that
way. A few programs can process zipped topologies and trajectories
(specifically cpptraj), but no program in Amber can process a zipped
tarball.
Unless you plan on sharing the files there's no reason to zip and tar.
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Mar 20 2014 - 05:00:04 PDT
