# [AMBER] Puzzles about calculating the binding energy of residues

From: Yanyan ZHU <zhuyanzily.gmail.com>
Date: Thu, 12 Dec 2013 22:10:40 +0800

Hi :
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
#
#####################################################################################################################
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Received on Thu Dec 12 2013 - 06:30:02 PST
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