AMBER Archive (2007)

Subject: Re: AMBER: fragment parametrization tutorial?

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Sun Sep 30 2007 - 02:12:41 CDT

Quoting "David A. Case" <case_at_scripps.edu>:

> On Sat, Sep 29, 2007, Carlos Simmerling wrote:
>
>> how about
>> *Simulating a Solvated Protein that Contains Non-Standard Residues*
>> http://www.rosswalker.co.uk/tutorials/amber_workshop/Tutorial_four/
>
> You might also look at:
>
> http://amber.scripps.edu/antechamber/example.html
>
> There is an example there of preparing a non-standard residue. (But we need
> to make things simpler than they are now.)

You might look at:
http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php
-I.3.2.3- Single- or multi-conformation multi-orientation RESP fits
for the central fragment of new amino-acids
-I.3.2.4- Multi-molecule multi-conformation multi-orientation RESP
fits for terminal fragments of new amino-acids

regards, Francois

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