AMBER Archive (2008)

Subject: Re: AMBER: MD of protein-ligand comlex

From: Chris Moth (chris.moth_at_vanderbilt.edu)
Date: Mon Jan 07 2008 - 06:10:23 CST

A few ideas:

This tutorial was written before antechamber and the GAFF forcefield were
developed.

It is still helpful as it shows you the lower level components that must
be thought through as you prepare your calculation.

For detailed receptor-ligand calculations, it is very important to
understand how new atom types are added to the forcefield, the likely
development of new forcefield parameters (bonds, angles, torsions)
required by your ligand, and the calculation of the ligand point charges.

Antechamber may be very helpful to you in development of these parameters.
 But for detailed calculations on a single ligand/receptor complex, you
will likely want to perform more detailed ligand parameterization.

> Hello amber users,
>
> I have few questions. I am trying to get Molecular Dynamic
> receptor-ligand complex. I have never done MD on protein-ligand complex
> before.
> I am studying Streptavidin/Biotin Tutorial and I am confused about how
> to do it.
> Should I create a " frcmod " file for my system?
> I do not understand why biotin file is prepared in leap . I thought, for
> preparation of ligand we need use Antechamber.
>
> Can someone please help?
>
>
> Thank you very much for any sugestions.
>
> Anna
>
>
> ---------------------------------
> Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it
> now.

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu