Re: [AMBER] Non-Standard Residue / Non-Integer Charge

From: David A Case <>
Date: Wed, 18 Mar 2015 20:32:35 -0400

On Tue, Mar 17, 2015, Maral Aminpour wrote:
> I tried to introduce two non-standard residues (Octyl group: C8H17 and
> Methyl: CH3) to a peptide sequence in Amber ...

Maybe *someday* we will get our non-standard residue tutorial (on green
fluorescent protein) finished....until then, go here:

and click on "generate residue topology for non-standard residues". This
shows how to do the charge manipulations you were doing by hand in a more
organized fashion.

The R.E.D. suite also has lots of tools for this task.

...good luck....dac

[Some Rutgers grad student or post-doc (or high school intern) could get
lots of brownie points, that later show in letters of reference, by taking
what we did in the boot camp and adding a minimal amount of polish. Getting
authorship credit for an Amber tutorial must be worth something....Sishi wrote
tutorial B4, and now she has a high-paying job at Goldman-Sachs. Just

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Received on Wed Mar 18 2015 - 18:00:02 PDT
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