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
> > >>>
> > >>>
> > >>> _______________________________________________
> > >>> AMBER mailing list
> > >>> AMBER.ambermd.org
> > >>> http://lists.ambermd.org/mailman/listinfo/amber
> > >>>
> > >>
> > >>
> > >
> > _______________________________________________
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> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Thu Oct 27 2016 - 09:30:07 PDT
