AMBER Archive (2009)

Subject: RE: [AMBER] Re: non aminoacid Residue

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Mon Jul 06 2009 - 11:21:44 CDT

Hi Neha,

> Well, this residue is connected at the ends with standard amino acid
> and
> hence if I use the gaff forcefield, it complains about the atom type
> between
> standard and non standard residue. If I use amber atom type then its
> complains about the N-N bond type wherein no such bond exists in the
> peptide.

You will need to build library files for the non-standard residues with head
and tail atoms defined and then they will get bound into the chain. You will
also need to provide parameters for everything, especially the connections.
If these are simply modified amino acids you are probably best off starting
with analogy to the existing FF99SB force field. The missing parameters you
will either need to find in the literature, derive yourself or guess!. Note
are you sure this has a N-N bond? Sounds pretty unstable to me.

Take a look at this tutorial
http://ambermd.org/tutorials/advanced/tutorial1_adv/ which will give you an
idea about how to create custom residues in leap etc.

All the best
Ross

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|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
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