AMBER Archive (2006)

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

From: Xioling Chuang (xioling_c_at_hotmail.com)
Date: Thu Jun 29 2006 - 23:16:48 CDT

Dear Cenk Andac

Many thanks for your ansers and suggestions. However, it is not quite clear
for me, as questions below.

>1). GBtot is binding free energy between two strands, isn't it?
> Delta GBtot= Delta Hgas + Delta Gsolvation
> you need to add 1.79 to Delta GBtot to get Delta H of binding.

You mean Delta H(binding) = Delta GBtot + 1.79 , right?
and what does 1.79 come from?

>2). If no, how can I calculate the binding free energy?
>
> If you use NM 1 option, then you should be able to see TSTOT (temp*Stot)
>in your mm-pbsa output.

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?

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?

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?

I am sorry for many questions since they are not clear for me. Thank you vey
much in advance again.

Best Regards,
Xioling

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