AMBER Archive (2008)

Subject: Re: AMBER: changing pdb structure

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Tue Nov 11 2008 - 05:35:42 CST

one possibility is to let leap do the DNA mutation on the pdb file that you
have already mutated the protein residue. delete from the pdb any atoms that
are not in the base that you want to have, leaving the common atoms. then
change the residue name of these atoms to what you want (DA?) and load into
leap. leap will add the missing ones. you then need to minimize/equilibrate
that region with the rest held fixed, etc, as with any mutation. I've done
DNA mutations with leap following the above and it works fine for an initial
model. of course some mutants will give a bad initial geometry for the base
pair (a mismatch, etc), and I don't know if Coot deals with that (would be
nice).

On Mon, Nov 10, 2008 at 4:10 PM, Taufik Al-Sarraj <
taufik.alsarraj_at_utoronto.ca> wrote:

> You are correct Carols,
> The program thinks it is an amino acid and not DNA. 1DGC contains a protein
> and DNA, protein mutation can be done (easily) in Sirius. However DNA
> mutation can not. Coot can do simple mutation for DNA only, but not for a
> system that contains DNA and a protein. I think it is mixing the two.
>
>
>
> Carlos Simmerling wrote:
>
>> I haven't been following this thread, but I'm wondering why a DNA mutation
>> would involve ALA and CA,C,N atoms... sounds like a protein. are you sure
>> it's DNA? apologies if this would be more clear if I'd read the previous
>> messages.
>>
>> On Mon, Nov 10, 2008 at 3:31 PM, Taufik Al-Sarraj <
>> taufik.alsarraj_at_utoronto.ca <mailto:taufik.alsarraj_at_utoronto.ca>> wrote:
>>
>> Hi Ibrahim,
>> Thank you for suggesting Coot. I am trying to do a DNA mutation
>> but unfortunately i have not been successful.
>> The error message i get is
>>
>> 'INFO:: mutate 2 to a ALA
>> DISASTER! Not all necessary atoms found in residue 2
>> CA is missing
>> C is missing
>> N is missing
>> failure to get orientation matrix'
>>
>> I tried the do mutation with a pdb structure from pdb.org
>> <http://pdb.org> 1DGC, and i tried to do a mutation on a dna
>> created using nucgen in amber. Both attempts gave me the error above.
>>
>> any help would be greatly appreciated.
>> Taufik
>>
>> Ibrahim Moustafa wrote:
>>
>> Hi Taufik,
>>
>> You can the program COOT
>>
>> http://www.ysbl.york.ac.uk/~emsley/coot/>
>> <http://www.ysbl.york.ac.uk/%7Eemsley/coot/>
>>
>> You should be able to modify the structure of your protein &
>> nucleic
>> acids. It is a straight forward program to use.
>> Also, chimera can do that too.
>>
>> HTH,
>> Ibrahim
>>
>>
>>
>> On 10/9/08 11:29 PM, "Ross Walker" <ross_at_rosswalker.co.uk
>> <mailto:ross_at_rosswalker.co.uk>> wrote:
>>
>>
>> Hi Taufik,
>>
>> I don't know if there is a specific program that can do
>> this, however, one
>> simple thing you can try is to edit the pdb and go to the
>> residue you want
>> to change. Delete all the atoms from this residue except
>> the backbone atoms
>> (and perhaps keep CB as well). Then change the name of the
>> residue to the
>> new residue you want and load it into leap. Leap will then
>> add all of the
>> missing atoms for this new residue.
>>
>> Note, this will of course leave you with steric clashes so
>> you may want to
>> relax the structure carefully by minimizing and then
>> running MD with
>> restraints on the modified residue etc.
>>
>> Good luck,
>> Ross
>>
>>
>> -----Original Message-----
>> From: owner-amber_at_scripps.edu
>> <mailto:owner-amber_at_scripps.edu>
>> [mailto:owner-amber_at_scripps.edu
>> <mailto:owner-amber_at_scripps.edu>] On Behalf
>> Of taufik.alsarraj_at_utoronto.ca
>> <mailto:taufik.alsarraj_at_utoronto.ca>
>> Sent: Thursday, October 09, 2008 7:35 PM
>> To: amber_at_scripps.edu <mailto:amber_at_scripps.edu>
>> Subject: AMBER: changing pdb structure
>>
>> Hello,
>> This is a general question.
>>
>> If i take a structure from the protein data bank, and
>> the structure
>> contains a protein and a DNA, is there a a software or
>> a relatively
>> simple method for modifying the protein sequence or
>> the DNA sequence,
>> e.g. changing an A to L (Protein) or changing a T to A
>> (DNA). Short of
>> manual modification in xleap or deleting the original
>> DNA and creating
>> a new one.
>>
>>
>> Best,
>> Taufik
>>
>>
>>
>>
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