# Re: [AMBER] MM-PBSA calculation in different temprature

From: Hai Nguyen <nhai.qn.gmail.com>
Date: Wed, 26 Oct 2016 14:24:55 -0400

"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:
>
> >
> > 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:
> >
> >>
> >>
> >> 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.
> >>>
> >>>
> >>>
> >>>
> >>> 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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Received on Wed Oct 26 2016 - 11:30:03 PDT
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