I agree with Carlos, and it is what the SCWRL from the Dunbrack lab does.
See see Shapovalov and Dunbrack, Proteins, 66:279-303 (2007)
Stephane
________________________________________
De : Carlos Simmerling [carlos.simmerling.gmail.com]
Date d'envoi : lundi 10 septembre 2012 21:17
À : AMBER Mailing List
Objet : Re: [AMBER] point mutation - residue swap
Oops - - invert "chirality".
Auto incorrect.
On Sep 10, 2012 3:01 PM, "Carlos Simmerling" <carlos.simmerling.gmail.com>
wrote:
> This isn't a good method- leap doesn't care at all where it puts the side
> chain and unless you're very lucky you will have bad steric clashes that
> can invert chivalry and other bad things. You want to use a program that
> searches rotamers for something that fits as best as possible.
> On Sep 10, 2012 2:48 PM, "FyD" <fyd.q4md-forcefieldtools.org> wrote:
>
>> Dear Jonathan,
>>
>> You could edit the PDB file: (i) remove the side chain of the amino
>> acid to be mutated; (ii) rename the backbone of this residue according
>> to the residue name of the mutation. Then, you load the modified PDB
>> file in the LEAP program, which will automatically add the missing
>> atoms (i.e. the side chain) in agreement with the FF library of the
>> mutated residue.
>>
>> regards, Francois
>>
>>
>> > The basic (or complex) question I have is:
>> >
>> > How do you take a PDB and change one residue to another residue?
>> > (essentially a point mutation of an existing structure)
>> >
>> > I thought I remembered reading how it could be done, but looking back I
>> > can't seem to find where it might be. I can think of a few ways one
>> could
>> > accomplish this, but I wanted to ask if there is an explanation in the
>> > manual or a tutorial that I am just missing. (Can someone point me in
>> the
>> > right direction)
>> >
>> > 1. I searched the archives and saw some old posts regarding using other
>> > programs.
>> > 2. One could manually add/change things
>> > 3+????
>> >
>> > Not necessarily looking for a step by step but a push in the right
>> > direction.
>>
>>
>>
>> _______________________________________________
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
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Received on Mon Sep 10 2012 - 13:00:03 PDT
