[AMBER] how to run non standard simulation

From: muhammad tahir ayub <tahirgp0.gmail.com>
Date: Mon, 27 Apr 2015 23:39:46 +0500

Dear Amber Users
                           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
I have completed first and 3rd tutorial.

*Muhammad Tahir*
*Ayub*

*Junior Research Fellow*

*H.E.J Research Institute of Chemistry*
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Received on Mon Apr 27 2015 - 12:00:03 PDT