If manual cleanup is needed, Leap actually has a useful minimizer that
has no vdw term, but can make adjustments to a few atoms at a time (the
more at a time, the harder to check). One can progressively clean up a
structure to one's taste by selecting and minimizing graphically.
Bill
On 9/10/2012 8:35 PM, Aron Broom 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.
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> _______________________________________________
>>>>>>>>>> AMBER mailing list
>>>>>>>>>> AMBER.ambermd.org
>>>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> AMBER mailing list
>>>>>>>>> AMBER.ambermd.org
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>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> --
>>>>>>>> Carmenza Martinez
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>> Carmenza Martinez
>>>>>>> _______________________________________________
>>>>>>> AMBER mailing list
>>>>>>> AMBER.ambermd.org
>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>>>
>>>>>> _______________________________________________
>>>>>> AMBER mailing list
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>>>>>
>>>>>
>>>>> --
>>>>> Aron Broom M.Sc
>>>>> PhD Student
>>>>> Department of Chemistry
>>>>> University of Waterloo
>>>>> _______________________________________________
>>>>> AMBER mailing list
>>>>> AMBER.ambermd.org
>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>
>>>> _______________________________________________
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>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>
>>>
>>>
>>> --
>>> Aron Broom M.Sc
>>> PhD Student
>>> Department of Chemistry
>>> University of Waterloo
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>>
>> --
>> With regards
>>
>> Vaibhav A. Dixit
>> Ph.D. Scholar
>> Department of Medicinal Chemistry
>> Natl. Inst. Pharm. Edu.& Res. (NIPER)
>> Sector 67, Phase X, S.A.S. Nagar (Mohali)
>> Punjab -160 062 INDIA
>> Phone (Mobile): +919915214408
>> E-mail: vaibhavadixit.gmail.com
>> www.niper.nic.in
>> _______________________________________________
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>>
>
>
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Received on Mon Sep 10 2012 - 21:00:03 PDT
