[AMBER] help in amber

From: Robin Jain <robinjain.chem.gmail.com>
Date: Wed, 8 Jul 2015 15:01:26 +0530

Dear all,
i have simulate a organic molecule in 128 methanol in a cubic box of 21
angstrom and after 60ns production , i want to use final coordinate for
abinitio md, Therefore i load my trajectory in VMD to save last frame
coordinates but after loading i saw that all the methanol molecules are too
much far away from each other and their coordinates are out of box, for
this i used another option given in Amber program such as ambpdb to save
coordinates but it also show to much variable coordinates , specially in
negative values. What is going wrong, Please help me in this regard.

Thanking You.

Robin Jain
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Received on Wed Jul 08 2015 - 03:00:02 PDT
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