Re: [AMBER] how to run non standard simulation

From: David A Case <case.biomaps.rutgers.edu>
Date: Mon, 27 Apr 2015 17:51:35 -0400

On Mon, Apr 27, 2015, muhammad tahir ayub wrote:

> I want to run the simulation of IKKb protein
> (PDB ID: 4KIK) along with different inhibitors. The 4KIK protein comprises
> histidine and modified residues like SEP (phosphorylated serine ). Are
> following tutorials are sufficient to follow for my protein
>
> 1)
> http://sf.anu.edu.au/collaborations/amber_on_fujitsu/amber-12/tutorial/standard-setup/index.html
> 2)
> https://sf.anu.edu.au/collaborations/amber_on_fujitsu/amber-12/tutorial/nonstandard-setup/index.html
> 3) http://ambermd.org/tutorials/basic/tutorial4b/
> 4) http://ambermd.org/antechamber/efz.html
>
> also i want to know that to know that what is the difference between the
> third and fourth tutorials while both tutorials are for the same ligand

The 4th example is an advanced version of the 3rd example. You will see that
the explanations in example 4 are very condensed, so it is more of a reference
than a tutorial.

Don't be afraid to try things; and don't expect everything to work the first
time.

...dac


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Received on Mon Apr 27 2015 - 15:00:02 PDT