Hi,
I have performed MD simulations of CCR2 with membrane (POPC). I have also
estimated per residue decomposition free energy using MM/GBSA method by
perl script. Residues which shows hydrophobic and hydrogen bond
interactions with ligand shows good decomposition free energy (about -8 to
-2 kcal/mol). But, glutamic acid which shows ionic interaction with the
quaternary nitrogen of ligand gives unfavorable decomposition free energy
(about 8 kcal/mol). Here I kept external and internal dielectric constant
values 80 and 1 respectively. Then, internal dielectric constant was
changed to 10 which gave decomposition free energy of glutamic acid about
-2.5kcal/mol.
Can anyone tell me what values should I use for internal dielectric
constant so I can get reasonable decomposition free energies for residues
showing both hydrophobic and ionic interactions?
Thanks in advance.
With regards,
Jignesh
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Received on Tue Jun 12 2012 - 04:30:03 PDT
