AMBER Archive (2008)

Subject: Re: AMBER: changing pdb structure

From: Taufik Al-Sarraj (taufik.alsarraj_at_utoronto.ca)
Date: Mon Nov 10 2008 - 14:31:39 CST

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 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/
>
> 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> 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] On Behalf
>>> Of taufik.alsarraj_at_utoronto.ca
>>> Sent: Thursday, October 09, 2008 7:35 PM
>>> To: 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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>
>
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