Quoting vaibhav dixit <vaibhavadixit.gmail.com>:
> That's great! Can this program be made available for academic use?
gedit & xLEaP will do the job; and they are free in the sense of freedom ;-)
regards, Francois
> On Tue, Sep 11, 2012 at 3:20 PM, Carlos Simmerling <
> carlos.simmerling.gmail.com> wrote:
>
>> yes this is easier- I've even written a program that resequences the DNA by
>> keeping the common atoms between old and new base and renaming them so leap
>> builds the rest. of course you can still get clashes, such as with purine
>> pairs, but at least it gives you a structure to start.
>>
>>
>> On Mon, Sep 10, 2012 at 11:35 PM, Aron Broom <broomsday.gmail.com> wrote:
>>
>> > I've never done this, but I would imagine this is a far simpler problem
>> > than the amino acid one, since the orientation of the bases should remain
>> > the same. Perhaps in this scenario the LEaP method would actually work
>> > just fine?
>> >
>> > On Mon, Sep 10, 2012 at 10:52 PM, vaibhav dixit <vaibhavadixit.gmail.com
>> > >wrote:
>> >
>> > > If I have a DNA or RNA lets say dodecamer, how can I mutate it? Means
>> how
>> > > can I replace A with G or T with C?
>> > > Thanks for your suggestions in advance.
>> > >
>> > > On Tue, Sep 11, 2012 at 6:02 AM, Aron Broom <broomsday.gmail.com>
>> wrote:
>> > >
>> > > > Yikes, point taken.
>> > > >
>> > > > Also for anyone who finds this thread, PyMol has a mutation function
>> > that
>> > > > uses a rotamer library.
>> > > >
>> > > > ~Aron
>> > > >
>> > > >
>> > > > On Mon, Sep 10, 2012 at 6:24 PM, Carlos Simmerling <
>> > > > carlos.simmerling.gmail.com> wrote:
>> > > >
>> > > > > what often happens in my experience is that the steric clashes are
>> > bad
>> > > > > enough that the atoms get pushed around, and the chirality inverts
>> > > > because
>> > > > > of that. eventually you minimize the clash away, but in the process
>> > > > things
>> > > > > are no longer correct. we've even seen really weird cases such as
>> > > where a
>> > > > > Phe ended up with a protein chain going through the middle of the
>> > ring-
>> > > > > obviously no way that will ever get fixed in MD.
>> > > > >
>> > > > > I guess I'm just warning people that if you have a high energy
>> > > structure,
>> > > > > just because you minimize it doesn't mean things are ok. you should
>> > > > always
>> > > > > visually inspect the area where you made the change.
>> > > > >
>> > > > >
>> > > > > On Mon, Sep 10, 2012 at 5:53 PM, Aron Broom <broomsday.gmail.com>
>> > > wrote:
>> > > > >
>> > > > > > Just as an addition/question here concerning the LEaP approach:
>> if
>> > > you
>> > > > > > delete everything EXCEPT the backbone AND beta-carbon (or in the
>> > case
>> > > > of
>> > > > > > mutating glycine to something, just rename the "sidechain"
>> hydrogen
>> > > to
>> > > > a
>> > > > > > carbon) would LEaP then use that and thereby avoid the problem of
>> > > > messing
>> > > > > > up chirality or something extreme, and leave you only with the
>> > > problem
>> > > > or
>> > > > > > steric clashes?
>> > > > > >
>> > > > > > If so, it's clearly not as ideal as using a program that has a
>> > > rotamer
>> > > > > > library as has been suggested here, but still isn't devestating
>> if
>> > > you
>> > > > > are
>> > > > > > willing to do some minimization or something or the sort.
>> > > > > >
>> > > > > > ~Aron
>> > > > > >
>> > > > > > On Mon, Sep 10, 2012 at 4:30 PM, Jonathan Gough
>> > > > > > <jonathan.d.gough.gmail.com>wrote:
>> > > > > >
>> > > > > > > Thank you all for your help! Very good suggestions. I am
>> using
>> > > > swiss
>> > > > > > PDB
>> > > > > > > right now.
>> > > > > > >
>> > > > > > > I said 3+ as I could think of at least 1 if not multiple more
>> > ways
>> > > to
>> > > > > do
>> > > > > > it
>> > > > > > > (other applications or combinations of applications).
>> > > > > > >
>> > > > > > >
>> > > > > > >
>> > > > > > > On Mon, Sep 10, 2012 at 3:43 PM, Carmenza Martinez <
>> > > > crm3680.gmail.com
>> > > > > > > >wrote:
>> > > > > > >
>> > > > > > > > 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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Received on Tue Sep 11 2012 - 06:00:03 PDT
