Dear community
I am facing a weird problem while running MMGBSA calculations on my
simulated protein-protein complex using Amber Tools 18.
My protein complex consists of protein 1 which is a dimer (residues 1 to
199; followed by a TER cut; 200-398), protein 2 (399 to 576) and protein 3
(577 to 754).
Proteins 2 and 3 are identical.
I want to calculate the binding affinity of protein 1 with 2 and 3
separately.
I am running the following compounds:
ante-MMPBSA.py -p clus1-1_wat.top -c complex1.top -r rec1.top -l lig1.top
-n :399-576 -s :WAT,Na+,Cl-
ante-MMPBSA.py -p clus1-1_wat.top -c complex2.top -r rec2.top -l lig2.top
-n :577-754 -s :WAT,Na+,Cl-
And then:
MMPBSA.py -O -i mmgbsa1.in -sp clus1-1_wat.top -cp complex1.top -lp
lig1.top -rp rec1.top -y ../imaged3.nc -o mmgbsa3a.dat -do decomp3a.dat >
mmgbsa3a.out &
and
MMPBSA.py -O -i mmgbsa1.in -sp clus1-1_wat.top -cp complex2.top -lp
lig2.top -rp rec2.top -y ../imaged3.nc -o mmgbsa3b.dat -do decomp3b.dat >
mmgbsa3b.out &
In both cases, the mmgbsa.dat file reads as:
| Run on Tue Oct 13 15:21:28 2020
|
|Input file:
|--------------------------------------------------------------
|MMPBSA.py input file for running GB
|&general
| startframe=1, endframe=5000, interval=2500,
| keep_files=0, netcdf=1,
|/
|&gb
| igb=5, saltcon=0.1
|/
|&decomp
| idecomp=4, dec_verbose=0, csv_format=0
|--------------------------------------------------------------
|MMPBSA.py Version=14.0
|Solvated complex topology file: clus1-1_wat.top
|Complex topology file: complex1.top
|Receptor topology file: rec1.top
|Ligand topology file: lig1.top
|Initial mdcrd(s): ../imaged3.nc
|
|Receptor mask: ":1-398,577-754"
|Ligand mask: ":399-576"
|
|Calculations performed using 2 complex frames.
|
|Generalized Born ESURF calculated using 'LCPO' surface areas
|
|All units are reported in kcal/mole.
Please help me identify where I am going wrong? Why isn't the ligand mask
changing?
Thanks
Suchetana
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Oct 14 2020 - 05:30:02 PDT
