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.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.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf
>> Of taufik.alsarraj.utoronto.ca
>> Sent: Thursday, October 09, 2008 7:35 PM
>> To: amber.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
>>
>>
>>
>> -----------------------------------------------------------------------
>> The AMBER Mail Reflector
>> To post, send mail to amber.scripps.edu
>> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
>> to majordomo.scripps.edu
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
> to majordomo.scripps.edu
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
to majordomo.scripps.edu
Received on Sun Oct 12 2008 - 05:12:52 PDT
