[AMBER] simulation of protein

From: ashutosh shandilya <izerokelvin.gmail.com>
Date: Fri, 4 Jun 2010 22:02:48 +0530

Hi All
I have a homology model of protein after minimization I ran a 2 ns md
equilibration.The RMSD is difference is about 4.5 angstrom with the original
one.My question is why it is happening and which structure is supposed to be
good for ligand design.
While heating for 150 ps at 300K RMSD difference was only 1 angstrom while
equilibration it changed a lot.

Thanks in advance
Ashutosh Shandilya
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Received on Fri Jun 04 2010 - 10:00:04 PDT
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