Right. ptraj does mutations? How did you get the mutant trajectory files?
2011/7/8 Jesper Sørensen <lists.jsx.dk>
> Thanks Dwight I will give it a go.
>
> Essentially, if I just made all the input files (mdcrd etc.) myself
> "manually" in ptraj and leap, and feed these into MMPBSA.py, there
> shouldn't
> be a problem, right?
>
> Best,
> Jesper
>
> -----Original Message-----
> From: Dwight McGee [mailto:dwight.mcgee.gmail.com]
> Sent: 6. juli 2011 17:01
> To: AMBER Mailing List
> Subject: Re: [AMBER] Ala double mutation scans
>
> Hi,
>
> If you wanted to make multiple mutations, the *perl version* of MMPBSA does
> allow for this. If you instead wanted to use the *python version* of MMPBSA
> and run a double alanine scanning calculation it would in essence take two
> steps. Step 1 would be mutating one residue to Ala and allowing MMPBSA.py
> to
> make the mutant mdcrd. Step 2 would be taking the new mutant mdcrd created
> in the previous step and reading it into MMPBSA.py using the (-y) flag ( be
> sure to use the correct topology files matching the mutant mdcrd) so
> therefore it will make the second mutant mdcrd, which will in essence have
> the double mutation you want. The tricky part is that you will have to
> create two new topology files, one containing the single mutation and the
> other one that has the double mutation. Hopefully this should work.
>
> 2011/7/6 Jesper Sørensen <lists.jsx.dk>
>
> > Hey all,
> >
> >
> >
> > I know that MMPBSA.py isn’t set up for double ala-scanning
> > calculation, but wouldn’t I be able to make the required files
> > manually and then just feed these into MMPBSA.py using the right keywords
> in the input file?
> >
> > I know that double mutations are probably stretching the methods
> > accuracy quite a bit as two mutations close together will probably
> > alter the dynamics, but I’d like to give it a go anyways.
> >
> >
> >
> > Are there alternative ways to do it? Like running one ala scan
> > calculation and then running a second one on the “new” trajectories
> > formed by MMPBSA.py.
> > And then just adding up the results?
> >
> >
> >
> > Best regards,
> >
> > Jesper
> >
> >
> >
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> >
>
>
>
> --
> T. Dwight McGee Jr.
> Quantum Theory Project
> University of Florida
> Graduate Student
> dwight.mcgee.gmail.com
>
> "Problems cannot be solved at the same level of awareness that created
> them."
> Albert Einstein
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
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Received on Sat Jul 09 2011 - 08:00:03 PDT
