sorry I meant to say just as Prof. Simmerling said...the said got
deleted...sorry
On Mon, Sep 10, 2012 at 3:39 PM, Carmenza Martinez <crm3680.gmail.com>wrote:
> Not sure if anybody has suggested it previously but for single point
> mutations or multiple mutations of residues I have found swissPDB to be
> quite useful:
> http://spdbv.vital-it.ch/
> Just as Prof. Simmerling leap is not efficient at filling in the blanks
> when you remove things and renamed them just as Francois suggested.
> Now, when you say 3+???? I don't understand what you mean...changing the
> protonation state perhaps? for that you will need more than what swiss PDB
> could provide. Perhaps somebody else in the forum will provide useful
> advide for that
> Best regards
>
>
>
> On Mon, Sep 10, 2012 at 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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>
>
> --
> Carmenza Martinez
>
>
--
Carmenza Martinez
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Received on Mon Sep 10 2012 - 13:00:04 PDT
