Re: [AMBER] Ala double mutation scans

From: Dwight McGee <dwight.mcgee.gmail.com>
Date: Mon, 11 Jul 2011 13:36:58 -0400

Hi,

Ptraj does not make the mutant mdcrd. The module alamdcrd.py creates the
mutant mdcrd. A more advanced way (if you want a stand-alone program) to
create a mutant mdcrd would be to use the program *make_crd.hg*, which is a
program used by the perl version of MMPBSA. You will need to create a file
called *make_crd.in*. I have attached an example of the format of the input.
You can refer to the Amber Manual and look in the MMPBSA perl version
section to understand what certain variables are like, *for example,
MUTANT_ATOM1* and the other variables should be self explanatory. The
program make_crd.hg will instead create coordinate files instead of a mdcrd,
so you can easily create a shell script that will write a ptraj input to *
trajin* all the coordinate files and *trajout* one mdcrd for you. Hope that
helps

2011/7/10 Jesper Sørensen <lists.jsx.dk>

> Ah, good point. I figured MMPBSA.py made the mdcrd files using ptraj - am I
> wrong?
> Is there a different tool that I can use then?
>
> Best,
> Jesper
>
> -----Original Message-----
> From: Jason Swails [mailto:jason.swails.gmail.com]
> Sent: 9. juli 2011 16:58
> To: AMBER Mailing List
> Subject: Re: [AMBER] Ala double mutation scans
>
> 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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> > > AMBER.ambermd.org
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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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> >
> >
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> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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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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Received on Mon Jul 11 2011 - 11:00:09 PDT
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