# [AMBER] Puzzles about calculating binding energy using MMGBSA

From: Yanyan ZHU <zhuyanzily.gmail.com>
Date: Sat, 14 Dec 2013 20:05:41 +0800

Hi all:

I am a graduate student in Sichuan university from China. I have some
puzzles as following: I want to calcuate the binding energy of residues
after calculating the integral binding energy of complex successfully. In
my input files,x-wat-com.prmtop, x-wat-pro.prmtop ,x-wat-lig.prmtop are the
prmtop of complex ,receptor and ligand respectively. And in my system , the
number of atom for complex, receptor and ligand are 4521, 4484 and 37
respectively. The dielectric constant of the composite solvent in my system
is 56.97.

My problem is that I can successfully calculate the binding energy
through the input file of coords.in and binding.in.in. However, I can not
achieve the calcuation of residues through the input file of coorsd.in and
resid.in.

I am looking for you replay and will be very grateful for your
kindhearted.

The three input files are as following:

##########################################################################################################################################

coords.in

.GENERAL

VERBOSE 0

PARALLEL 0

#

PREFIX wat

PATH ./

START 1

STOP 100

OFFSET 1

#

COMPLEX 1

RECEPTOR 1

LIGAND 1

#

COMPT ./x-wat-com.prmtop

RECPT ./x-wat-pro.prmtop

LIGPT ./x-wat-lig.prmtop

#

GC 1

AS 0

DC 0

#

MM 0

GB 0

PB 0

MS 0

#

NM 0

.MAKECRD

BOX NO

NTOTAL 4521

NSTART 1

NSTOP 100

NFREQ 1

#

NUMBER_REC_GROUPS 1

RSTART 1

RSTOP 4484

NUMBER_LIG_GROUPS 1

LSTART 4485

LSTOP 4521

.TRAJECTORY

TRAJECTORY ./7-com.mdcrd

######################################################################################################################################

binding.in

.GENERAL

VERBOSE 0

PARALLEL 0

#

PREFIX wat

PATH ./

START 1

STOP 100

OFFSET 1

#

COMPLEX 1

RECEPTOR 1

LIGAND 1

#

COMPT ./x-wat-com.prmtop

RECPT ./x-wat-pro.prmtop

LIGPT ./x-wat-lig.prmtop

#

GC 0

AS 0

DC 0

#

MM 1

GB 1

PB 0

MS 1

#

NM 0

#

.PB

PROC 2

REFE 0

INDI 1.0

EXDI 56.97

SCALE 2

LINIT 1000

ISTRNG 0.0

INP 2

#

SURFTEN 0.04356

SURFOFF -1.008

#

IVCAP 0

CUTCAP -1.0

XCAP 0.0

YCAP 0.0

ZCAP 0.0

#

.MM

DIELC 1.0

#

.GB

IGB 2

GBSA 1

SALTCON 0.00

EXTDIEL 56.97

INTDIEL 1.0

#

SURFTEN 0.0072

SURFOFF 0.00

#

.MS

PROBE 0.0

#

#############################################################################################################################

resid.in

.GENERAL

VERBOSE 0

PARALLEL 0

#

PREFIX wat

PATH ./

START 1

STOP 100

OFFSET 1

#

COMPLEX 1

RECEPTOR 1

LIGAND 1

#

COMPT ./x-wat-com.prmtop

RECPT ./x-wat-pro.prmtop

LIGPT ./x-wat-lig.prmtop

#

GC 0

AS 0

DC 1

#

MM 1

GB 0

PB 1

MS 0

#

NM 0

#

.DECOMP

#

DCTYPE 2

#

COMREC 1-276

COMLIG 277-277

COMPRI 1-276 277-277

RECRES 1-276

RECPRI 1-276

RECMAP 1-276

LIGRES 1-1

LIGPRI 1-1

LIGMAP 277-277

#

.PB

PROC 2

REFE 0

INDI 1.0

EXDI 56.97

SCALE 2

LINIT 1000

ISTRNG 0.0

INP 0

#

SURFTEN 0.04356

SURFOFF -1.008

#

IVCAP 0

CUTCAP -1.0

XCAP 0.0

YCAP 0.0

ZCAP 0.0

#

.MM

DIELC 1.0

#

.GB

IGB 2

GBSA 2

SALTCON 0.00

EXTDIEL 56.97

INTDIEL 1.0

#

SURFTEN 0.0072

SURFOFF 0.00

#

.MS

PROBE 0.0

#

##############################################################