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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>
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Received on Fri Sep 23 2016 - 07:30:03 PDT
