Hi Geng,
MMPBSA.py mutates the coordinates directly. If you look through the code
you may be able to write a Python script to call the relevant function
without running MMPBSA.py. However, it still requires you to build the
alanine-mutated topology file with tleap beforehand.
HTH,
Jason
On Sun, Oct 17, 2021 at 8:52 AM Matthew Guberman-Pfeffer <
matthew.guberman-pfeffer.uconn.edu> wrote:
> Hi Geng,
>
> A quick idea, though there are probably more rigorous ways of doing this:
> Use the change command in ParmEd to zero out the non-bonded terms for the
> sidechain atoms except the beta carbon. Then, use the change command in
> ParmEd to give the beta carbon effective charge and LJ parameters to mimic
> the methyl of alanine. Finally, write a new topology file. This altered
> topology can be used with your original trajectory to assess the energy
> (e.g., with esander).
>
> Best,
> Matthew
>
> > On Oct 17, 2021, at 5:32 AM, 东庚 <gdong.stu.edu.cn> wrote:
> >
> > *Message sent from a system outside of UConn.*
> >
> >
> > Hi all,
> > I would to calculate the difference of nonbond interaction between
> wildtype and mutation (to alanine) protein. I have a trajectory for
> wildtype. Can I generate a mutated (to alanine) trajectory, directly. I
> know that the mutated trajectory can be generated by mmpbsa.py in alanine
> scanning calculation. What program is used in mmpbsa.py?
> > Best,
> > Geng
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Jason M. Swails
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Received on Fri Oct 29 2021 - 06:30:09 PDT
