AMBER Archive (2006)

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

From: Xioling Chuang (xioling_c_at_hotmail.com)
Date: Fri Jun 30 2006 - 23:39:09 CDT

Dear jenk,

Thank you very much for your kind answers.

Best Regards,
xioling

>From: Cenk Andac <cenk_andac_at_yahoo.com>
>Reply-To: amber_at_scripps.edu
>To: amber_at_scripps.edu
>Subject: Re: AMBER: How to calculate binding free energy using MM-PBSA
>Date: Fri, 30 Jun 2006 05:22:08 -0700 (PDT)
>
>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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