Dear All
I want to run the MMPBSA.py calculation for my QM/MM simulations. I am
having a small issue while running this calculation. below is my input file
&general
startframe=1, endframe=1000, interval=100, verbose=2, keep_file=0,
use_sander=1
/
&gb
igb=5, saltcon=0.100,
ifqnt=1, qm_residues="211,249,252,281,545,546,568", qmcharge_lig=0,
qmcharge_rec=-1, qmcharge_com=-1,
qm_theory="PM6"
/
Previously I ran this file a few months ago and ran without any problem.
However now it gives me the error of
You most likely have the charge of : System specified with odd number of
electrons ( 427) but odd spin ( 1). ) QM region (qmcharge) set incorrectly
I have checked the charges in Gaussian and I get 0 charges on complex,
ligand and receptor but receptor and complex are doublets while ligand is
singlet.
I ran the same parameters in MMPBSA.pl and it is not showing any problem.
because of this AMBER is showing the calculation error with water stripped
complex file. Also the same old issue of the mdins disappearing once I use
the -use-mdins command.
I am using AMBER 12 and AMBER TOOLS 13.
Anyone has suggestions? I am attaching the top part of my previously run
file
------------------------------------------------------------------
Run on Thu Jul 23 13:23:28 2015
|
|Input file:
|--------------------------------------------------------------
|&general
|startframe=1, endframe=5000, interval=100, verbose=2, keep_file=0,
use_sander=1
|/
|&gb
|igb=5, saltcon=0.100,
|ifqnt=1, qm_residues="211,249,252,281,545,546,568", qmcharge_lig=0,
qmcharge_rec=-1, qmcharge_com=-1,
|qm_theory="PM6"
|/--------------------------------------------------------------
|MMPBSA.py Version=13.0
|Solvated complex topology file: ../jzw33.prmtop
|Complex topology file: ../jz33.top
|Receptor topology file: ../prot33.top
|Ligand topology file: ../zer33.prmtop
|Initial mdcrd(s): ../1ns.mdcrd
| ../2ns.mdcrd
|
|Receptor mask: ":1-567"
|Ligand mask: ":568"
|Ligand residue name is "ZER"
|
|Calculations performed using 20 complex frames.
|
|Generalized Born ESURF calculated using 'LCPO' surface areas
|
|All units are reported in kcal/mole.
|QM/MM: Residues 211,249,252,281,545,546,568 are treated with the Quantum
Hamiltonian PM6
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
GENERALIZED BORN:
Complex:
------------------------------------
Thank you
Ayesha Fatima
UM, Malaysia
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Received on Thu Apr 21 2016 - 09:00:03 PDT
