H i Jason Swails :
Thanks for your kindhearted again.
Firstly, We can not successfully calculating the binding energy of
each 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 not achieve the calcuation the binding energy of
each residue through the input file of coorsd.in and resid.in. The two
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
###########################################################################################################
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
PRBRAD 1.4
ISTRNG 0.0
RADIOPT 1
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
#
##############################################################
The error is as following:* bad atom type : hn. We have tried
the *MMPBSA.py
as you mentioned, however the error is identical to the MMPBSA.pl.
Then we tried to examine the Amber12 as you mentioned to solve the
problem of calculating the binding energy of each residue . We made sure
that the AMBERHOME points to our Amber 12 release and the Amber 12
bin/ directory
appears in our PATH variable before the Amber 11 bin/ directory. However,
we found that AMBER11 was invoked in our output files for the process of
molecular dynamic simulation. Besides that , the molecular dynamic
simulation process which invoked AMBER11 ,could not calculate the binding
energy of each residue.
Thanks for your advice and looking for your reply.
YANYAN ZHU
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Received on Sat Dec 21 2013 - 20:30:02 PST
