Re: [AMBER] Multiple ligands in MMGBSA from Elvis Martis on 2017-01-31 (Amber Archive Feb 2017)

From: Elvis Martis <elvis.martis.bcp.edu.in>
Date: Wed, 1 Feb 2017 03:13:13 +0000

See this tutorial http://ambermd.org/tutorials/advanced/tutorial24/ its on Free energy workflow. It might be helpful

[http://ambermd.org/tutorials/advanced/tutorial24/figures/Table1.gif]<http://ambermd.org/tutorials/advanced/tutorial24/>

Amber Tutorial A24 - FEW<http://ambermd.org/tutorials/advanced/tutorial24/>
ambermd.org
Figure 1: Schematic depiction of setup of MD simulations with FEW. Input information used in this tutorial is highlighted in blue, input data that may be required for ...

                   Best Regards

[photo]

Elvis Martis
Ph.D. Student (Computational Chemistry)
at Bombay College of Pharmacy

A Kalina, Santacruz [E], Mumbai 400098, INDIA
W www.elvismartis.in<https://webapp.wisestamp.com/www.elvismartis.in>
Skype. adrian_elvis12<https://webapp.wisestamp.com/#>

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________________________________
From: Abhilash J <md.scfbio.gmail.com>
Sent: 31 January 2017 21:50:05
To: AMBER Mailing List
Subject: [AMBER] Multiple ligands in MMGBSA

Hi everyone!

  I want to run MM GBSA on a trajectory. My complex has 7 ligands. All
ligands are identical but at different positions. They have different
residue numbers. How can i calculate the MMGBSA energy for a specific
ligand residue.
  Is it possible to calculate MMGBSA energy for all ligands in a single run
of MMGBSA.

Regards

Abhilash
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Received on Tue Jan 31 2017 - 19:30:02 PST