AMBER Archive (2008)

Subject: RE: AMBER: adding missing residues

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Thu Jul 24 2008 - 07:35:41 CDT

Hi Soumick,

You can edit your pdb files and add the alpha carbons for each of the
missing residues. .eg. just add the single atom for each missing residue.
Then when you load the pdb in leap it will build in the remaining missing
atoms based on the templates it has. Note, though that you will need to come
up with some coordinate estimates for the alpha carbons and you will have to
carefully minimize / equilibrate the residues that were added since their
initial structures will be highly strained.

Good luck,
Ross

> -----Original Message-----
> From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
> Of soumick
> Sent: Thursday, July 24, 2008 4:09 AM
> To: amber_at_scripps.edu
> Subject: AMBER: adding missing residues
>
> Hi,
>
> Could you please tell me how can i add missing residues in amber? My
> protein has got two Chain A and B. I have some missing residues. I tried
> adding the residues in CAChe, but it is seperating the chains appart. The
> missing residues are begining of the chain A and B.
>
> Thanks
> Soumick
>
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
> to majordomo_at_scripps.edu

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu