The qmmask define residues ligand or residues that you want to treat with
QM parameter and rest of protein ligand system will be treated with MM
parameter. Generally people put ligand and active site residues as QM mask
as people are more inetersted in precise MD of active site using QM
parameter. You can use some tutorials for that
1.
http://ambermd.org/tutorials/advanced/tutorial2/section3.htm
2.
http://sf.anu.edu.au/collaborations/amber_on_fujitsu/amber-12/tutorial/qm-mm/index.html
On Mon, May 19, 2014 at 11:53 AM, Nitin Sharma <sharmanitin.nus.edu.sg>wrote:
> Thanks Soumendranath,
>
> Till now I was not using qmmm mask while minimizing. Can you and others
> enlighten me on the importance of using it and is it mandatory to use for
> good results.
>
> Thanks, Nitin
>
> -----Original Message-----
> From: Soumendranath Bhakat [mailto:bhakatsoumendranath.gmail.com]
> Sent: Monday, May 19, 2014 4:29 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] QM/MM based binding free energy analysis AMBER
>
> As per my understanding goes in QM/MM molecular dynamics you must treat
> some active site residues and ligand with QM mask with some keywords. Rest
> part of your simulation goes via MM. In QM there are different algorithms
> to parameterize but based on one report I presume DFTB-SCC is the best one.
> Then you should perform and generate .mdcrd file based on QM/MM molecular
> dynamics protocols with keywords specific. And then add QM keywords in the
> GBSA or PBSA script to perform binding free energy based on QM/MM method.
> Some inputs I already shared in the mailing list but I asked for
> confirmation of these scripts. I am resharing them again please amber
> developers or some experts verify these scripts.
>
> Full_Mini.in
>
> Initial minimization of QMMM: solvent molecules and added ions &cntrl
> imin = 1,
> maxcyc = 2500,
> ncyc = 750,
> ntb = 1,
> ntr = 1,
> cut = 12.0,
> ifqnt = 1,
> /
> &qmmm
> qmmask= '250,238.75,86,89,75',
> qmcharge=0,
> qmtheory=1, *(please suggest number based on DFTB-SCC)* qmshake=1,
> qm_ewald=1, qm_pme=1, /
>
> Hold the Protein fixed
> 10.0
> RES 1 557
>
> Heating.in
>
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> *Heating Step of QMMM: stage-2 &cntrl imin= 0, irest=0, NTX=1, ntb=
> 1, NTPR=500, NTWX=500, NTWR=500, ntr=1, Tempi=0.0, Temp0=300.0,
> ifqnt=1, NTT=3, gamma_ln=1.0, NTC=2, NTF=2, cut= 12.0,
> nstlim=2500, dt=0.002,/&qmmmqmmask=
> '250,238.75,86,89,75',qmcharge=0,qmtheory=1,qmshake=1,qm_ewald=1,qm_pme=1,
> /Keep Protein and inhibitor fixed with weak restraints10.0RES 1 557ENDEND*
>
> equil.in
>
> Equilibration Step of MMP3 (MMMM): stage-1 &cntrl
> imin= 0,
> irest=1,
> NTX=7,
> ntb=2,
> ntp=1,
> PRES0=1.0,
> TAUP=2.0,
> NTPR=500,
> NTWX=500,
> ntr=0,
> Tempi=300.0,
> Temp0=300.0,
> NTT=3,
> ifqnt=1,
> gamma_ln=1.0,
> NTC=2,
> NTF=2,
> cut=12.0,
> nstlim=250000,
> dt=0.002
> /
> &qmmm
> qmmask= '250,238.75,86,89,75',
> qmcharge=0,
> qmtheory=1,
> qmshake=1,
> qm_ewald=1,
> qm_pme=1,
> /
> *md.in <http://md.in>*
> Equilibration Step of MMP3 (MMMM): stage-1 &cntrl
> imin= 0,
> irest=1,
> NTX=7,
> ntb=2,
> ntp=1,
> PRES0=1.0,
> TAUP=2.0,
> NTPR=500,
> NTWX=500,
> ntr=0,
> Tempi=300.0,
> Temp0=300.0,
> NTT=3,
> ifqnt=1,
> gamma_ln=1.0,
> NTC=2,
> NTF=2,
> cut=12.0,
> nstlim=2500000,
> dt=0.002
> /
> &qmmm
> qmmask= '250,238.75,86,89,75',
> qmcharge=0,
> qmtheory=1,
> qmshake=1,
> qm_ewald=1,
> qm_pme=1,
> /
>
> *MMGBSA script*
>
> Input file for running PB and GB in serial &general startframe=1,
> endframe=5000, interval=5verbose=2,entropy=1,keep_file=0,
> /
> &gb
> igb=5,saltcon=0.15,ifqnt=1,qmmask= '250,238.75,86,89,75',
> qmcharge=0,qmtheory=1, /
>
>
>
>
> On Mon, May 19, 2014 at 1:30 AM, Nitin Sharma <sharmanitin.nus.edu.sg
> >wrote:
>
> > Hello Soumendranath,
> >
> > I went through few papers and followed the approach mentioned in J
> > Comput Chem 32: 866-877, 2011 . I did minimization of the water and
> > then of the selected residues + ligand in consecutive steps. Then I
> > created .mdcrd file from minimized structure and calculated MMGBSA
> > energy. However, as you results were scary.
> >
> > Let me know your inputs on my approach and the paper I mentioned
> >
> > Best,
> > Nitin
> >
> > -----Original Message-----
> > From: Soumendranath Bhakat [mailto:bhakatsoumendranath.gmail.com]
> > Sent: Monday, May 19, 2014 3:48 AM
> > To: AMBER Mailing List
> > Subject: Re: [AMBER] QM/MM based binding free energy analysis AMBER
> >
> > Hii Nitin;
> >
> > Thats a bit of scary data 1000 kcal/mol. Though I am looking at some
> > papers saying for QM/MM GBSA or PBSA such as
> > http://www.ncbi.nlm.nih.gov/pubmed/24490903 and
> > http://www.ncbi.nlm.nih.gov/pubmed/24631364
> >
> > Did u perform a QM/MM based MD taking catalytic and crucial residues
> > treated with QM parameter and then perform QM/MM GBSA or PBSA? Because
> > 1000 kcal/mol is the most false approximation ever.
> >
> >
> > On Mon, May 19, 2014 at 1:08 AM, Nitin Sharma <sharmanitin.nus.edu.sg
> > >wrote:
> >
> > > Hello Soumendranath,
> > >
> > > I just worked on same thing and didn't get what I was expecting
> > > after reading all the papers recommending MMGBSA method over other
> > > scoring methods. I wished to rescore docking poses after
> > > minimization BUT to my surprise I got energy values more than 1000
> > > Kcal/mol which I found
> > amusing.
> > > Moreover, there was no trend in the values. Hence, I moved to
> > > rescore with docking software
> > >
> > >
> > > Do let me know if you have some tips to improve the results
> > >
> > > Best,
> > > Nitin
> > >
> > > -----Original Message-----
> > > From: Soumendranath Bhakat [mailto:bhakatsoumendranath.gmail.com]
> > > Sent: Monday, May 19, 2014 3:30 AM
> > > To: AMBER Mailing List
> > > Subject: [AMBER] QM/MM based binding free energy analysis AMBER
> > >
> > > Dear Amberists;
> > >
> > > It has been noticed that recent developments in QM/MM based
> > > parametirization raised some better approximation of binding free
> > > energy close to experimental counterpart. For literature:
> > > http://www.ncbi.nlm.nih.gov/pubmed/22210962
> > >
> > > Literature and some other trails suggested that DFTB-SCC level QM/MM
> > > approximation might leads to a better approximation than MM one.
> > >
> > > I am just qurious if AMBER developers tried some test runs to check
> > > the effect of QM/MM based free energy calculations compared to
> > > experimental one for a better approximation of binding free energy?
> > >
> > >
> > > --
> > > Thanks & Regards;
> > > Soumendranath Bhakat
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > > _______________________________________________
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> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> > --
> > Thanks & Regards;
> > Soumendranath Bhakat
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Thanks & Regards;
> Soumendranath Bhakat
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--
Thanks & Regards;
Soumendranath Bhakat
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Received on Mon May 19 2014 - 03:30:03 PDT
