AMBER Archive (2006)

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

From: Cenk Andac (
Date: Fri Jun 30 2006 - 07:22:08 CDT

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,

Yahoo! Messenger with Voice. Make PC-to-Phone Calls to the US (and 30+ countries) for 2/min or less.
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to