Thank you very much. I will try mmpbsa.py.
________________________________
From: Jason Swails <jason.swails.gmail.com>
To: bin wang <wang_p_z.yahoo.com.cn>; AMBER Mailing List <amber.ambermd.org>
Sent: Friday, November 11, 2011 10:22 PM
Subject: Re: [AMBER] comparison failures in the Amber11 and AT15 test
If you ran the AT15_Amber11.py script, it printed this at the bottom:
NOTE: Because PBSA has changed since Amber 11 was released, some
tests are known to fail and others are known to quit in error. These
can be safely ignored.
Tests that error: Tests in $AMBERHOME/test/sander_pbsa_frc
Run.argasp.min Run.dadt.min Run.dgdc.min
Run.lysasp.min Run.polyALA.min Run.polyAT.min
Run.argasp.min Run.dadt.min Run.dgdc.min
Run.lysasp.min Run.polyALA.min Run.polyAT.min
Run.argasp.min Run.dadt.min Run.dgdc.min
Run.lysasp.min Run.polyALA.min Run.polyAT.min
Tests that produce possible FAILUREs:
cd sander_pbsa_ipb2 && ./Run.110D.min
cd sander_pbsa_lpb && ./Run.lsolver.min (only some of them fail here)
cd sander_pbsa_tsr && ./Run.tsrb.min
cd sander_pbsa_decres && ./Run.pbsa_decres
mm_pbsa.pl tests 02, 03, and 05
Also note that you'll have much better luck getting support for problems
with MM/PBSA analyses if you use the Python version of the script
(MMPBSA.py, which is part of AmberTools 1.5).
HTH,
Jason
On Fri, Nov 11, 2011 at 6:20 PM, bin wang <wang_p_z.yahoo.com.cn> wrote:
> Dear Amber users,
> I have a question regarding the test of Amber11 and AT15.
> After installation of AT15 and Amber11, I run make test and get the .diff
> files in folder $AMBERHOME/AmberTools/test/logs/test_at_serial and
> $AMBERHOME/test/logs/test_amber_serial. The results showed some comparison
> failures. Especially, there are some possible failures in
> test/sander_pbsa_radi, test/sander_pbsa_tsr, test/sander_pbsa_decres,
> test/sander_pbsa_decpw, and src/mm_pbsa/Examples. But I need to use pbsa
> to calculate binding energy. I am wondering if these failures are
> significant problems? Can I still use mm_pbsa or I have to fix it?
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon Nov 14 2011 - 11:30:03 PST
