AMBER Archive (2009)

Subject: Re: [AMBER] MMGBSA IG Value

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Fri Mar 20 2009 - 12:25:38 CDT

do you mean igb, not ig? ig is for the random number generator, igb is for
the GB solvent model.
I suggest finding a study that worked well on a system similar to your for
similar goals, and use that as a guide. it will be very hard to jusify your
choice to journal reviewers if you say "I chose this based on an email
list". check the peer-reviewed literature.

having said that, here is some advice:
I suggest igb=5 along with mbondi2 radii, this has worked well for me.
and yes, the PBradii are also used for GB, so it is important to choose the
one you want. different radii are best with different GB models, so again,
check the literature to see what has worked for others.

On Fri, Mar 20, 2009 at 1:20 PM, Rajesh Raju <
Rajesh.Raju_at_postgrad.manchester.ac.uk> wrote:

> Hi,
>
> I want to do MMGBSA free enrgy decomposition and binding energy
> calculations for my protein-ligand system. Which IG option (IG=1, 2, 5 )
> should i use ? Can i use the same paramter file for IG=1 and IG =2 .
>
> I read somewhere inorder to use IG =2 I should use the leap command
>
> ''set default PBradii bondi'' when setting up the prmtop file? But I have
> dount that I am doing MMGBSA (not PBSA). So should I modify the prmtop file?
>
> Cheers
>
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber