[AMBER] MMPBSA

From: Sourav Purohit <sour000.gmail.com>
Date: Mon, 14 Apr 2014 12:05:29 +0530

Hi All,
One more question just to make sure that my procedure is correct.
Th efollowing has been done in the MMPBSA tutorial:

 com = loadpdb ras-raf.pdb
ras = loadpdb ras.pdb
raf = loadpdb raf.pdb

 set default PBRadii mbondi2

saveamberparm com ras-raf.prmtop ras-raf.inpcrd
saveamberparm ras ras.prmtop ras.inpcrd
saveamberparm raf raf.prmtop raf.inpcrd

 I wanted to know if the sequence of commands is fixed. i.e . will it be
correct if I use the "set default PBRadii" command before loading the pdb
files??

Please help.

Thanks.
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Received on Mon Apr 14 2014 - 00:00:02 PDT
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