Hi,
Please see amber manual + see the tutorial here:
http://ambermd.org/tutorials/advanced/tutorial3/py_script/section1.htm
As far as I understand, you don't need to change your mmpbsa input, you
only need to change your trajectory name (run from different T).
Hai
On Thu, Oct 27, 2016 at 12:13 PM, shahab shariati <shahab.shariati.gmail.com
> wrote:
> Dear Hai,
>
> Thank you.
>
> I want to know the content of in file for my favourite temperature?
>
> Please guide me about that.
>
> Best,
> Shahab
>
>
> On Wed, Oct 26, 2016 at 9:54 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:
>
> > I think you already got the reply about this.
> >
> > Re-quote from Adrian
> > "Technically yes, you have to RERUN the MD at the new temperature and
> > rerun mmpbsa"
> >
> > I guess you need to rerun the mmpbsa with new trajectory from the new
> > temperature run.
> > So the only difference here is the difference between old and new
> > trajectory (same other mmgbsa inputs)
> >
> > Hai
> >
> > On Wed, Oct 26, 2016 at 2:18 PM, shahab shariati <
> > shahab.shariati.gmail.com>
> > wrote:
> >
> > > Dear amber users,
> > >
> > > How to do MM-PBSA calculation in different temperature other than 25 or
> > 298
> > > K?
> > >
> > > On Tue, Oct 25, 2016 at 1:59 PM, shahab shariati <
> > > shahab.shariati.gmail.com>
> > > wrote:
> > >
> > > > Dear Adrian,
> > > >
> > > > I did md simulation in temperature = 340 K using following in file:
> > > >
> > > > ------------------------------------------------------------
> > > > ------------------------
> > > > prod1_complex_solvated
> > > > &cntrl
> > > > imin=0,irest=1,ntx=5,
> > > > nstlim=2500000,dt=0.002,
> > > > cut=10.0,ntb=2,ntp=1,taup=2.0,
> > > > ntc=2,ntf=2,
> > > > ntpr=2500,ntwx=2500,
> > > > ntt=3,gamma_ln=2.0,
> > > > temp0=340.0,
> > > > /
> > > > ------------------------------------------------------------
> > > > ------------------------
> > > >
> > > > I want to do mmgbsa calculation in temperature = 340 K.
> > > >
> > > > I used following input file:
> > > >
> > > > ------------------------------------------------------------
> > > > ------------------------
> > > > Input file for running PB
> > > > &general
> > > > startframe=10, endframe=4000, interval=100,
> > > > verbose=1, keep_files=1,
> > > > entropy=1,
> > > > ntt=3,gamma_ln=2.0,
> > > > temp0=340.0,
> > > > /
> > > > &gb
> > > > igb=2, saltcon=0.100,
> > > > /
> > > > ------------------------------------------------------------
> > > > --------------------------
> > > >
> > > > But, I encountered with
> > > >
> > > > InputError: Unknown variable ntt in &general
> > > > Enter `MMPBSA.py.MPI --help` for help
> > > > ------------------------------------------------------------
> > > > --------------------------
> > > >
> > > > How to change the temperature in mmgbsa?
> > > >
> > > > How to resolve this problem?
> > > >
> > > > On Fri, Sep 23, 2016 at 5:33 PM, shahab shariati <
> > > > shahab.shariati.gmail.com> wrote:
> > > >
> > > >> Dear Adrian,
> > > >>
> > > >> Thanks for your quick answer.
> > > >>
> > > >> I will use the following in file for MM-PBSA calculation:
> > > >>
> > > >> ------------------------------------------------------------
> > > >> -----------------
> > > >> Input file for running PB
> > > >> &general
> > > >> startframe=10, endframe=4000, interval=100,
> > > >> verbose=1, keep_files=1,
> > > >> entropy=1,
> > > >> /
> > > >> &gb
> > > >> igb=2, saltcon=0.100,
> > > >> /
> > > >> &pb
> > > >> istrng=0.100,
> > > >> /
> > > >> ------------------------------------------------------------
> > > >> ------------------
> > > >>
> > > >> For different temperatures, should I use "temp0=310.0" in the &cntrl
> > > >> namelist like what is in the in file for MD?
> > > >>
> > > >> ------------------------------------------------------------
> > > >> ------------------
> > > >> prod1complex_solvated
> > > >> &cntrl
> > > >> imin=0,irest=1,ntx=5,
> > > >> nstlim=2500000,dt=0.002,
> > > >> cut=10.0,ntb=2,ntp=1,taup=2.0,
> > > >> ntc=2,ntf=2,
> > > >> ntpr=2500,ntwx=2500,
> > > >> ntt=3,gamma_ln=2.0,
> > > >> temp0=310.0,
> > > >> /
> > > >> ------------------------------------------------------------
> > > >> -----------------
> > > >>
> > > >> Best regards,
> > > >> Shahab
> > > >>
> > > >> On Fri, Sep 23, 2016 at 4:15 PM, Adrian Roitberg <roitberg.ufl.edu>
> > > >> wrote:
> > > >>
> > > >>> Technically yes, you have to RERUN the MD at the new temperature
> and
> > > >>> rerun mmpbsa. You should not reuse the MD at 298 and simply change
> > the
> > > >>> temperature in mmbpsa.
> > > >>>
> > > >>> However, it is extremely unlikely that you will see statistically
> > > >>> meaningful differences between 298 and 310 with mmbpsa.
> > > >>>
> > > >>> Adrian
> > > >>>
> > > >>>
> > > >>>
> > > >>> On 9/23/16 7:07 AM, shahab shariati wrote:
> > > >>> > Dear amber users,
> > > >>> >
> > > >>> > I want to calculate the binding free energy of several
> > protein-ligand
> > > >>> > complexes in two temperatures 298 and 310 K using MMPBSA.py in
> > > >>> Ambertools
> > > >>> > 14.
> > > >>> >
> > > >>> > Can I do that (My main question is about the temperature)?
> > > >>> >
> > > >>> > Any help will highly be appreciated.
> > > >>> > _______________________________________________
> > > >>> > AMBER mailing list
> > > >>> > AMBER.ambermd.org
> > > >>> > http://lists.ambermd.org/mailman/listinfo/amber
> > > >>>
> > > >>> --
> > > >>> Dr. Adrian E. Roitberg
> > > >>> University of Florida Research Foundation Professor.
> > > >>> Department of Chemistry
> > > >>> University of Florida
> > > >>> roitberg.ufl.edu
> > > >>> 352-392-6972
> > > >>>
> > > >>>
> > > >>> _______________________________________________
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> > > >>> AMBER.ambermd.org
> > > >>> http://lists.ambermd.org/mailman/listinfo/amber
> > > >>>
> > > >>
> > > >>
> > > >
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Received on Thu Oct 27 2016 - 10:30:02 PDT
