AMBER Archive (2004)

Subject: AMBER: solvation energy

From: hj zou (hjzou_at_iris3.simm.ac.cn)
Date: Tue Mar 30 2004 - 06:55:20 CST

Dear David £¬
      Thank you for your rapid reply.
      I calculate the solvation free energy by using mmpbsa.
      here is the input file:

################################################################################
@GENERAL
#
PREFIX m0
PATH ./
#
COMPLEX 0
RECEPTOR 0
LIGAND 1
#
LIGPT ./lig.top
#
GC 0
AS 0
DC 0
#
MM 1
GB 0
PB 1
MS 1
#
NM 0
#
################################################################################
@DELPHI
#
FOCUS 0
INDI 1.0
EXDI 80.0
PERFIL 80.0
SCALE 2
LINIT 1000
BNDCON 4
CHARGE ../my_amber94_delphi.crg
SIZE /userdata/hjzou/ab/neu/new1/my_parse_delphi.siz
#
SURFTEN 0.00542
SURFOFF 0.092
#
################################################################################
@MS
#
# Molsurf parameters
#
# PROBE - Radius of the probe sphere used to calculate the SAS.
# RADII - Name of the radii file.
#
PROBE 1.4
RADII /userdata/hjzou/ab/neu/new1/atmtypenumbers
#
#################################################################################
@PROGRAMS
#
# Program executables and paths
#
DELPHI /usr/people/guest/sxzheng/amber7/delphi/delphi
#
################################################################################

        here is the output:
state1:
charge:-1e

# MEAN STD
# =======================
ELE 11.27 0.00
VDW 21.26 0.00
INT 32.88 0.00
GAS 65.41 0.00
PBSUR 2.03 0.00
PBCAL -88.58 0.00
PBSOL -86.55 0.00
PBELE -77.30 0.00
PBTOT -21.13 0.00
state2:
charge:0e
# MEAN STD
# =======================
ELE -44.34 0.00
VDW 21.48 0.00
INT 37.28 0.00
GAS 14.42 0.00
PBSUR 2.05 0.00
PBCAL -18.20 0.00
PBSOL -16.15 0.00
PBELE -62.54 0.00
PBTOT -1.73 0.00

   I just wanna know the exact absolut solvation free energy of the ligand(oleic acid).I take the PBSOL as the solvation free energy of the ligand. The result does not seem to be resonable,then what's wrong with the calculation?
   A paper has reported the solvation of acetate ion(-76.79) and acetic acd(-6.70).In my opinion,the solvation free energy of fatty acid will increase as the length of that decreases. But I don't know the precise relationship between them ,linear?hyperbolic?
   Any suggestions are highly appreciated.
best regards
*************************************
hjzou
555 Zu Chong Zhi Road, Zhangjiang Hi-Tech Park
Drug Discovery and Design Center
Shanghai Institute of Materia Medica
Chinese Academy of Sciences
Shanghai 201203, China
Tel£º +86-21-50806600-1201
E-mail: hjzou_at_mail.shcnc.ac.cn
*************************************

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