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
> >
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Jul 10 2011 - 06:30:04 PDT
