AMBER Archive (2007)

Subject: AMBER: Abnormality in MM-PBSA result

From: msubhamoy_at_ibab.ac.in
Date: Fri Oct 19 2007 - 10:01:16 CDT

Respected Sir

I just want to know the reason of this abnormality. I have calculated the
binding free energy of
A-U (10 mers) and have got some abnormal results.

One would typically expect to find an extremely favourable electrostatic energy
and a dis-avourable solvation free energy. This symbolises the energy that ones
has to use to de-solvate the binding particles and to align their binding
interfaces.

But in my case its opposite? why is it so? Is it normal? or is it becoz of some
error I have made.

 MY REULTS

# DELTA
# -----------------------
# MEAN STD
# =======================
ELE 4676.18 84.25
VDW -106.62 6.41
INT 0.00 0.00
GAS 4569.56 84.90
PBSUR -13.15 0.34
PBCAL -4652.66 82.89
PBSOL -4665.81 82.77
PBELE 23.52 7.85
PBTOT -96.25 6.01
GBSUR -13.15 0.34
GB -4615.11 83.56
GBSOL -4628.26 83.44
GBELE 61.07 7.06
GBTOT -58.70 5.07

Here ELE component is positive where as PBCAL is negative . Why?

                                                                        s.mukerjee

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu