AMBER Archive (2006)

Subject: Re: AMBER: How to calculate binding free energy using MM-PBSA

From: Cenk Andac (cenk_andac_at_yahoo.com)
Date: Fri Jun 30 2006 - 07:22:08 CDT

Hi,
 
I would recommend that you read
 Gohlke et al. 2004 JCC,25,238
 to get all details about how mm-pbsa parameters are set up for yor particular case.
 
>You mean Delta H(binding) = Delta GBtot + 1.79 , right?
>and what does 1.79 come from?
 
 1.79 is a correction energy term due to six translational + rotational degrees of freedom
 (6*1/2RT=1.79 kcal/mol at 300 K) also see Gohlke et al. 2004 JCC,25,238.
 
 
 
>Can I run in one step (i.e. by setting MM=1, GB=1, PB=1, MS=1, NM=1)
>or I need to run MM,GB,PB and MS first, then run NM?
 yes, you can run all options above in one step.
 
 
>More questions concerning parameters,
>Q1) In MM, I set DIELC=1.0, whereas I set INTDI=4.0 for PB, INTDIEL=4.0 for
>GB and DIELC=4.0 for NM. I got error message as "INT != DIELC" Do I need
>to set all dielectric parametes as the same value?
 INDI ought to be 1 as well.
 Just an additional info , DIELC is 4 for NM set.
 
>Q2) For GB, I have seen someone set SURFOFF=0.92 and amber's example set
>SURFOFF=0.00. What should be use for this parameter?
 SURFOFF is 0.0 for the GB set and SURFOFF is 0.92 for the PB set.
 hope this helps,
 
 jenk.
 
 

                 
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