[AMBER] Pairwise energy calculations in cpptraj

From: Aishani Prem <aishaniprem.gmail.com>
Date: Mon, 24 Apr 2017 20:07:52 -0700

Hi,
     I am using 'pairwise' to calculate the van der waals and electrostatic
energy between the backbone atoms in my proteins.
My input file looks like:
trajin pdb_md1_.mdcrd
pairwise :1-56.N,CA,C,O out energy.out time 0.1

and I run the command :
$AMBERHOME/bin/cpptraj -p pdb_vac.prmtop -i vdwaal.trajin

The energy values that I get in my output file is unexpectedly high
(~84000kJ/mol) when I add in the backbone atoms in the mask. Is there
anything wrong with the calculations? 

-- 
Thank You and Regards,
Aishani Chittoor Prem
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Received on Mon Apr 24 2017 - 20:30:03 PDT
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