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I would like to calculate the binding energy of a peptide to a protein
that contains 4 Zn atoms. I have constructed the corresponding
topologies of the complex, receptor (both with Zn ions) and the
ligand. I am using the amber11 version of mm_pbsa.pl and I am
enclosing the input below:
I have set RADIOPT 0 and INP 1 according to the instructions to read
the radii from the topology file. I checked - they are there.
However the program reaches the point of creating a pqr file and stops
at the first Zn atom because it cannot find the radius:
=>> Calculating energy / entropy contributions
Calc contrib for ../01_GenerateSnapshots/phd_dpf3_com.crd.1
Checking atom numbers
Calc MM/GB/SAS
Generate PDB
Center PDB
Calc PBSA
Generate PQR
No radius found for Zn 2019 in residue ZNB 135
I would be grateful if anyone knows how to fix this problem.
Thanks,
Rami
Here is the mm_pbsa.in
# Input parameters for mm_pbsa.pl
#
# Holger Gohlke
# 25.02.2010
#
################################################################################
.GENERAL
#
VERBOSE 0
PARALLEL 0
#
PREFIX phd_dpf3
PATH ../01_GenerateSnapshots/
START 1
STOP 10
OFFSET 1
#
COMPLEX 1
RECEPTOR 1
LIGAND 1
#
COMPT ../phd_dpf3_anal.top
RECPT ../phd_anal.top
LIGPT ../h3k14_anal.top
#
GC 0
AS 0
DC 0
#
MM 1
GB 1
PB 1
MS 1
#
NM 0
#
################################################################################
.PB
#
PROC 2
REFE 0
INDI 1.0
EXDI 80.0
SCALE 2
LINIT 1000
PRBRAD 1.4
ISTRNG 150
RADIOPT 0
INP 1
#
SURFTEN 0.00542
SURFOFF 0.9200
#
IVCAP 0
CUTCAP -1.0
XCAP 0.0
YCAP 0.0
ZCAP 0.0
#
################################################################################
.MM
#
DIELC 1.0
#
################################################################################
.GB
#
IGB 5
GBSA 1
SALTCON 0.15
EXTDIEL 80.0
INTDIEL 1.0
#
SURFTEN 0.0072
SURFOFF 0.00
#
################################################################################
.MS
#
PROBE 0.0
#
################################################################################
Roman Osman
roman.osman.mssm.edu
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Received on Wed Nov 03 2010 - 09:30:04 PDT
