From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Sat Aug 13 2011 - 01:29:04 CDT
You have already been advised to not cross post to multiple lists. It's also very clear that you should spend some time reading the tutorials and manuals, into which went a great amount of work precisely to prevent numerous repetitive questions such as your own, and also becoming familiar with the logic and output of NAMD. It is not CHARMM and trying to force it to behave as such defeats the purpose of using it.
i still don't understand why you can't use the DCD trajectory file for your analysis, which, as was pointed out already, would be a significantly faster, more efficient, and more natural method. Even if for some strange reason you require PDB files, they can still be created through post-processing the DCD.
As to your latest specific question, maybe you should take a moment to understand what a coor file (typically) is and what a pdb file is. Then, I hope, you will understand why they are not interconvertible from simple command line functions.
On Aug 13, 2011, at 1:11 AM, Babban Mia wrote:
> I was suggested that .coor file can be simply converted to pdb format by typing the following in the terminal or bash shell script.
> cp myfile.coor myprot.pdb
> I tried but it does not seem to work.Please advise further
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