On Tue, Jan 5, 2016 at 12:39 AM, Manjula Saravanan <manjusimba.gmail.com>
wrote:
> *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 m
>
> e to sort out this problem.
>
You can always introduce geometric restraints (see the NMR chapter of the
Amber manual, which has a section on adding constraints). However, if you
need to use geometric constraints to prevent an interaction from breaking,
it either means that the interaction really is not as strong as you
initially thought *or* the model you are using has serious deficiencies
with respect to that interaction. Without a good understanding of the
underlying cause, it will be difficult to derive meaningful conclusions
from such a calculation.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Jan 05 2016 - 05:00:03 PST
