AMBER Archive (2006)

Subject: AMBER: Charge of the phosphorylated Ser/Thr in MM_PBSA calculation

From: zgleo (zgleo_at_tom.com)
Date: Thu Feb 16 2006 - 00:04:47 CST

Dear amber users£¬
    I want to calculate the binding free energy of a protein (222 AA) with a 7-AA peptide, in which a phosphorylated Thr (pThr) is included. The pThr is -2 charged according to the parameters contributed by Sticht et al. (http://pharmacy.man.ac.uk/amber/). However, the value of PBTOT given by MM_PBSA method is very large (-134.65 kcal/mol). I guess that the electrostatic energy between pThr and the protein may be estimated too much under contium solvent model. Any suggestion is welcome!

 

# COMPLEX RECEPTOR LIGAND
# ----------------------- ----------------------- -----------------------
# MEAN STD MEAN STD MEAN STD
# ======================= ======================= =======================
ELE -7721.30 42.67 -7209.03 43.95 -177.59 8.02
VDW -980.30 20.38 -927.82 20.13 1.01 2.98
INT 4786.40 46.57 4625.89 47.10 160.51 7.55
GAS -3915.20 48.01 -3510.96 51.07 -16.07 11.34
PBSUR 60.11 0.81 60.30 0.79 5.91 0.07
PBCAL -3876.45 31.21 -3789.96 32.87 -346.11 6.82
PBSOL -3816.33 31.03 -3729.66 32.89 -340.20 6.83
PBELE -11597.75 28.53 -10998.99 21.75 -523.69 4.87
PBTOT -7731.54 36.46 -7240.62 40.49 -356.26 9.14

# DELTA
# -----------------------
# MEAN STD
# =======================
ELE -334.69 16.98
VDW -53.49 4.50
INT 0.00 0.00
GAS -388.18 15.86
PBSUR -6.09 0.08
PBCAL 259.62 15.61
PBSOL 253.53 15.61
PBELE -75.07 11.08
PBTOT -134.65 8.52
 

Best regard!

¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡zgleo
¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡2006-02-16
___________________________________________
    
Zhiguo Liu
Ph.D candidate
Drug Discovery and Design Center
Shanghai Institute of Materia Medica
Chinese Academy of Science
Shanghai, China
zhiguo.leo_at_gmail.com
zgliu_at_sibs.ac.cn
___________________________________________

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