AMBER Archive (2009)

Subject: RE: [AMBER] Do I need to modify the cap residues

From: Ross Walker (
Date: Mon Apr 06 2009 - 12:00:05 CDT

Hi Nicholus,

If you want standard N and C terminal end groups then you do not need to do
anything. Leap should take care of this. However, if you want different
things such as neutral end groups or ACE / NME caps then you will need to
modify the pdb.

All the best

-----Original Message-----
From: [] On Behalf
Of nicholus bhattacharjee
Sent: Monday, April 06, 2009 9:45 AM
To: AMBER Mailing List
Subject: [AMBER] Do I need to modify the cap residues

Dear community,
                          I wanted to know that do I need to modify the
first and the last residues in a given PDB file to make it caped? Non of the
tutorials have told about this thing. They only say about modifyins CYS, HIS
residues. Please inform me about this and if I have to then what is the

Thanking you,

Nicholus Bhattacharjee
PhD Scholar
Department of Chemistry
University of Delhi
Delhi-110007 (INDIA)
Phone: 9873098743(M)
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