*With Best Regards*
*S. Manjula*
*Research Scholar*
*Laboratory of Biocrystallography and Computational Molecular Biology*
*Department of Physics*
*Periyar University*
*Salem-11*
*Tamilnadu*
---------- Forwarded message ----------
From: Manjula Saravanan <manjusimba.gmail.com>
Date: Tue, Jan 5, 2016 at 11:03 AM
Subject: Requesting clarifications about QM/MM minimization
To: amber.ambermd.org
Dear Sir/Madam,
I am currently trying to run the AMBER QM/MM minimization
of a protein ligand- complex obtained from the docking analysis
(Schrodinger software). I have set the 3000 maximum minimization steps.
while analyzing the minimization output pdb, I have found that the ligand
is missing some important H-bonding interactions in the active site that is
found in both the docking analysis as well as the crystal structure.
My QM/MM minimization input file is:
QM\MM Minimization
&cntrl
imin=1, maxcyc=3000, ncyc=1000,
cut=15, ntb=1, ntc=1, ntpr=100,
ifqnt=1
/
&qmmm
qmmask='.1533-1536,2569-2579,2219-2224,4461-4466,8693-8699,8772-8804'
qmcharge=0,
qmcut=15.0,
qm_theory='PM3',
qmshake=0,
writepdb=1,
qm_ewald=1, qm_pme=1
/
My question is, how to retain the protein-ligand inter
molecular interactions in the active site during the QM/MM minimization
process. Herewith I have attached the QM/MM minimization input file,
protein-ligand complex pdb (before qm/mm minimization), QM/MM minimized
structure. Kindly help me to sort out this problem.
Thanks in well advance.
*With Best Regards*
*S. Manjula*
*Research Scholar*
*Laboratory of Biocrystallography and Computational Molecular Biology*
*Department of Physics*
*Periyar University*
*Salem-11*
*Tamilnadu*
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Received on Mon Jan 04 2016 - 22:00:03 PST
