AMBER Archive (2008)

Subject: Re: AMBER: changing pdb structure

From: Taufik Al-Sarraj (taufik.alsarraj_at_utoronto.ca)
Date: Mon Nov 24 2008 - 17:37:24 CST

Hi Carlos,

Just to close this thread. coot can do DNA mutation. I had to make the
following changes to the pdb file in order to achieve this:

change O5' by O5*
                C5' by C5*
                O4' by O4*
                C4' by C4*
                C1' by C1*
                C2' by C2*
                O3' by O3*
                DT by Td
                DA by Ad
                DG by Gd
                DT by Td
and for Td, C7 by C5M

Pierre Aller suggested this and it worked!

Best,
Taufik

Carlos Simmerling wrote:
> 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 <mailto: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>
> <mailto: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>
> <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/>
> <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>
> <mailto: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>>
> [mailto: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>
> <mailto: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>
> <mailto: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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