question of MMPBSA calculation combined NAMD and APBS software

From: baogen duan (dbaogen_at_gmail.com)
Date: Thu Oct 11 2012 - 20:52:22 CDT

Dear NAMD users and developers,

          I want to calculate the binding energy between protein and small
molecule using NAMD and APBS software. But the result is weird. The
absolute value of binding energy is very large which is about thousands of
kJ/mol. In general, the value is about tens of kJ/mol. whether did I make a
mistake in the course of calculation. The calculation procedure is as
follow:

(1) Emm part using NAMD, whether is Emm part in gas phase calculated
without PBC defined in configure file. And the confiure file is :

*## ADJUSTABLE PARAMETERS*
*set inputname
atp
structure ./$inputname.psf
coordinates
./$inputname.pdb
set temperature
310
firsttimestep 0 *
* *
*## SIMULATION PARAMETERS
*
*# Input
paraTypeCharmm on
parameters ./par_all27_prot_na.prm
temperature $temperature*

*# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 14.0 *
*switching on
switchdist 12.0
pairlistdist 16.0*

*# Integrator Parameters
timestep 2.0 ;# 2fs/step
rigidBonds all ;# needed for 2fs steps
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 1*

*# Constant Temperature Control
langevin on ;# do langevin dynamics
langevinDamping 1 ;# damping coefficient (gamma) of 1/ps
langevinTemp $temperature
langevinHydrogen off ;# don't couple langevin bath to hydrogens*
**
*## EXECUTION SCRIPT*
*run 0*
**
Is the above configure file of Emm calculation in gas phase rignt?

(2) solvation free energy using APBS, the atom charge, radius, epsilon are
come from CHARMM 22 force field, the follow is a part of parameter file as
a input for APBS calculation
*# Format:
# <RESIDUE> <ATOM> <CHARGE> <RADIUS> <EPSILON>
# where <RESIDUE> is the residue name, <ATOM> is the atom name, <CHARGE>
# is the atomic charge in e, <RADIUS> is the van der Waals radius in
# A, and <EPSILON> is the van der Waals well depth in kJ/mol.*
*ALA N -0.470000 1.8500 0.8360
ALA HN 0.310000 0.2245 0.1923
ALA CA 0.070000 2.2750 0.0836
ALA HA 0.090000 1.3200 0.0920
ALA CB -0.270000 2.0600 0.3344
ALA HB1 0.090000 1.3200 0.0920
ALA HB2 0.090000 1.3200 0.0920
ALA HB3 0.090000 1.3200 0.0920
ALA C 0.510000 2.0000 0.4598
ALA O -0.510000 1.7000 0.5016*

Would you like to give me some help. Thanks in advance.

Best wishes,
Yours sincerely,

Duan Baogen

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