AMBER Archive (2008)

Subject: Re: AMBER: changing pdb structure

From: Ibrahim Moustafa (I.moustafa_at_psu.edu)
Date: Fri Oct 10 2008 - 09:24:30 CDT

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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