Hii;
What I will suggest is that you heat your system from tempi=0k to
temp0=300k and then equilibrate at 300k. From equil.rst start 5 different
MD trajectories with different initial velocities each with 2ns duration.
You can easily do it with this MD input. just beware of the keyword ig=-1
and temi and tempo.
Equilibration Step of MMP3 (MMMM): stage-1
&cntrl
imin= 0,
irest=0,
ig=-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,
gamma_ln=1.0,
NTC=2,
NTF=2,
cut=12.0,
nstlim=5000000, (edit here)
dt=0.002
/
Then do the mmgbsa for each 2ns run. Which will lead you to 5 different
mmgbsa,observe the trend and take the average. This technique is good for
ranking of inhibitors.
In another way, for very accurate analysis run 10 ns continuous MD, take
binding free energy from 0-500 ps, 0-1ns, 0-1.5ns and so on till 10ns and
check for convergence. You can extend to check convergence but it will
hardly converge so it is just for accuracy. Though you can proceed with
previously mentioned way.
On Tue, May 6, 2014 at 9:08 PM, Nitin Sharma <sharmanitin.nus.edu.sg> wrote:
> Hello Soumendranath,
>
> Do you mean that I should calculate binding free energy from 0-1ns , 0-2ns
> and so on using the frames till the limit i.e.1ns and 2ns in the cases
> mentioned OR you mean calculating binding free energy using the frame at
> 1ns, 2ns and so on.
>
> I wish to apply binding free energy to rank inhibitors and it is possible
> that different ligand have good correlation at different time. In that case
> which value I should use? Initially I planned to get binding free energy
> fot 5 trajectories and rank inhibiotrs on basis on average binding free
> energy with lowest energy indicating strong inhibitor.
>
> Waiting for your suggestions
>
> Regards,
> Nitin
>
> -----Original Message-----
> From: Soumendranath Bhakat [mailto:bhakatsoumendranath.gmail.com]
> Sent: Tuesday, May 06, 2014 11:23 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] number of frames in MMPBGBSA
>
> I have some doubts about your input as you are running 10ns you can easily
> calculate it by taking average frames from starting to last. At a
> particular frame if you want to calculate on the frame by frame basis then
> it should go well. For a better binding free energy approximation you
> should calculate at certain(at each nanoseconds, say for example binding
> free at 1ns, 2ns, 3ns, 4ns and ... then check the convergence) intervals
> and make a plot to check convergence. Individual frame or average frame is
> not a good way if you want to do a proper work.
>
> Though here is a script which might help you in running both MD and MMGBSA
>
> Equilibration Step of MMP3 (MMMM): stage-1 &cntrl
> imin= 0,
> irest=0,
> ig=-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,
> gamma_ln=1.0,
> NTC=2,
> NTF=2,
> cut=12.0,
> nstlim=5000000,
> dt=0.002
> /
>
> Input file for running PB and GB in serial &general startframe=1,
> endframe=10000, interval=10,keep_file=0, verbose=1, entropy=1, / &gb
> igb=5,saltcon=0.15, / &decomp idecomp=1,
> print_res="557;82;175;216;93;221;214;222;223;224;90;305;89;176;166;167;177;88;87;168",
> dec_verbose=1,csv_format=0,
> /
>
>
> On Tue, May 6, 2014 at 2:15 PM, Nitin Sharma <sharmanitin.nus.edu.sg>
> wrote:
>
> > Dear amber users,
> >
> > I ran a simulation of 10ns with following parameters
> >
> > Molecular dynamic simulation for 10ns
> > &cntrl
> > imin=0,
> > ntx=5,
> > irest=1,
> > ntpr=5000,
> > ntwr=50000,
> > ntwx=5000,
> > ioutfm=1,
> > ntxo=2,
> > nstlim=5000000,
> > dt=0.002,
> > ntt=1,
> > tautp=10.0,
> > temp0=310.0,
> > ntp=1,
> > pres0=1,
> > ntc=2,
> > ntf=2,
> > ntb=2,
> > cut=8.0,
> > /
> >
> > If I am correct the number of frames (snapshots) are nstlim/ ntwx
> > =5000000/5000=1000
> >
> > Now I calculated binding free energy and something in the output
> > confused me. It says Calculations performed using 2 complex frames BUT
> > as I have not mentioned interval variable. whose default value is 1,
> > the total frames should have been 501. Am I wrong ? by the way I am
> > using AMBER12
> >
> > Input file:
> > |--------------------------------------------------------------
> > |Input file for running GB
> > |&general
> > | startframe=500, verbose=1,entropy=1, / &gb
> > | igb=2, qm_theory = 'PM3', saltcon=0.100 / &decomp
> > | idecomp=2, dec_verbose= 2
> > |/
> > |--------------------------------------------------------------
> > |MMPBSA.py Version=13.0
> > |Solvated complex topology file: complex_solvated_noIons.prmtop
> > |Complex topology file: complex.prmtop
> > |Receptor topology file: receptor.prmtop
> > |Ligand topology file: ligand.prmtop
> > |Initial mdcrd(s): 5md_b_strip.mdcrd
> > |
> > |Receptor mask: ":1-154"
> > |Ligand mask: ":155"
> > |Ligand residue name is "UNK"
> > |
> > |Calculations performed using 2 complex frames.
> > |
> > |Generalized Born ESURF calculated using 'LCPO' surface areas
> > |
> > |All units are reported in kcal/mole.
> > |All entropy results have units kcal/mol (Temperature is 298.15 K).
> >
> >
> > I hope someone can clear my doubt.
> >
> > Thanks and regards,
> > Nitin Sharma
> > Department of Pharmacy,Faculty of Science,National University of
> > Singapore,block S7, Level 2, 18 science drive 4, Singapore 117543,
> > Republic of Singapore:
> > sharmanitin.nus.edu.sg<mailto:sharmanitin.nus.edu.sg> ; Phone
> > +6582969643; http://www.linkedin.com/in/imsharmanitin
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Thanks & Regards;
> Soumendranath Bhakat
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>
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--
Thanks & Regards;
Soumendranath Bhakat
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Received on Tue May 06 2014 - 11:30:07 PDT
