AMBER Archive (2008)

Subject: Re: AMBER: changing pdb structure

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Mon Nov 10 2008 - 14:37:32 CST

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> 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 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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>
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