AMBER Archive (2007)

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

From: Esther Brugger (esther_brugger_at_yahoo.com)
Date: Thu Mar 01 2007 - 13:15:51 CST

Thanks for your help. I add igb=1 in the input file, but I get another problem. Since in my intial mdcrd files, they have the counter ions and water molecules, now I remove the ions and water molecules and get the new mdcrd trajactory file by Ptraj in order to get SASA. When I run the Sander, it shows "bad atom type" that are corresponding to the counter ions. But If I didn't use prmtop, it shows: Unit 8 Error on OPEN: prmtop ( I think prmtop probably should not be ignored).
 What I should do now? I really want to solve this problem to get the SASA.
 
 Thanks a lot for your help!
 
"David A. Case" <case_at_scripps.edu> wrote: 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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Esther B.

 
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