Hi Hai,
Thanks for your response. I got the same ddG from both Gb and PB. SO I
doubt that it is igb issue. But I will give it a try. I am not sure how
people handle this protein interfaces with more than two chains. Any
information would be helpful.
Jag
On Mon, Oct 24, 2016 at 2:15 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:
> hi
>
> is the ddG number (1000 kcal/mol) from GB or PB calculation? If from GB
> (igb=8), can you give it a try with igb=5 (to make sure
> there is no bug with igb=8 code). But other might know better than I do
> with MMPB(GB)SA.
>
> Hai
>
> On Mon, Oct 24, 2016 at 2:03 PM, Jag Silwal <jagsilwal.gmail.com> wrote:
>
> > Dear all,
> >
> > I ran a simulation for protein complexes which includes four chains as
> > shown below. Protein "C" is a dimer and protein A binds to protein C and
> I
> > am interested to run MM-PBSA to estimate binding free energy between
> > protein A and protein C in its dimeric form.
> > Fo MM-PBSA, I created a separate PDB file for A and another PDB file with
> > the rest of the proteins (C-C dimer +another A). Then for the MMPBSA
> > command I treated A as the ligand protein and C-C dimer + A as receptor
> > protein. I ran with the following script:
> >
> >
> > &general
> > |startframe=4501, endframe=5550, interval=5,
> > |verbose=2, keep_files=2, strip_mask=':WAT,CL',
> > |/
> > |&gb
> > |igb=8, saltcon=0.150,
> > |/
> > |&pb
> > |inp=1, radiopt=0, istrng=0.15, fillratio=4.0
> > |/
> >
> >
> > When the run was done I checked the Delta delta G and it came to be about
> > 1000 kcal/mol which I think is way too high for the interface.
> > Previously, I have separately ran and analyzed the Delta delta G without
> > the dimer where there is only one A and one C the Delta delta G was -60
> > kcal/mol.
> >
> > So I am sure I am not either setting these different PDBs right or may
> be I
> > am missing something important while setting up for MM-PB/GBSA analysis.
> > How do I approach this problem?
> >
> > Any insight would be really appreciated.
> >
> >
> >
> > [image: Inline image 2]
> >
> >
> >
> >
> >
> > Sincerely,
> >
> > Jag
> > Graduate Student,
> > Michigan State University
> > Department of Chemistry
> >
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> >
> >
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Received on Mon Oct 24 2016 - 16:30:03 PDT
