AMBER Archive (2008)

Subject: Re: AMBER: problem:capping

From: David A. Case (case_at_scripps.edu)
Date: Sun Jan 13 2008 - 11:10:55 CST

On Sun, Jan 13, 2008, jani sahil wrote:

> i am new to amber and i am facing a problem in capping the n terminal and c
> terminal residue of a protein about 329 residue long

Typical capping residues are ACE and NME. You will probably have to manually
edit your pdb file to assign the N atom (now in residue 1) to ACE and convert
one of the O atoms (now in residue 329) to NME. Then LEaP can build in the
missing atoms.

This is just a schematic set of instructions, since I don't know what your PDB
file looks like. Play around with this until you get what you want.

...dac

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