AMBER Archive (2007)

Subject: Re: AMBER: solvent accessible surface area (SASA)

From: David A. Case (case_at_scripps.edu)
Date: Thu Mar 01 2007 - 12:42:31 CST

On Thu, Mar 01, 2007, Esther Brugger wrote:

> I remove the water by using ptraj, and doing the calcuation as following:
>
> $AMBERHOME/exe/sander -O -i 1_SASA.in -c 1_initial.rst -p 1_wat.prmtop -x 1_SASA.mdcrd -o LV_SASA.out
>
> After runing it, it shows:
> GB/SA calculation is performed only when igb>0
>
> I really don't know which option I should select in igb. Could you please give me some suggestions?
>

I don't think it matters: as I understand this, you are planning to ignore
everything but the SASA calculation anyway. (Please ignore my comment if this
assumption is not correct.) So just set igb=1.

...dac

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