Hi Ross,
Yes or no ... it depends on whether you want to use sander for mmpbsa
types of calculations. I'll change the code in Amber10/sander anyway.
But pb_sasa.f is supposed to be deleted from the Amber9 cvs tree.
All the best,
Ray
Ross Walker wrote:
>Hi Ray,
>
>A quick question. Does this same patch need to be applied to the sa-driver.f
>file in the sander src directory as well?
>
>There is also the same logic on line 379 of $AMBERHOME/src/pb_sasa.f
>
>I assume this will need the same patch?
>
>All the best
>Ross
>
>/\
>\/
>|\oss Walker
>
>| HPC Consultant and Staff Scientist |
>| San Diego Supercomputer Center |
>| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
>| http://www.rosswalker.co.uk | PGP Key available on request |
>
>Note: Electronic Mail is not secure, has no guarantee of delivery, may not
>be read every day, and should not be used for urgent or sensitive issues.
>
>
>
>>-----Original Message-----
>>From: owner-amber-developers.scripps.edu
>>[mailto:owner-amber-developers.scripps.edu] On Behalf Of Ray Luo
>>Sent: Tuesday, May 02, 2006 12:20
>>To: amber-developers.scripps.edu
>>Subject: Re: amber-developers: AMBER 9 Problems on IRIX and ALTIX
>>
>>Here is the bugfix. This should've been caught in Amber8 ... I don't
>>understand why it is okay with most compilers.
>>
>>Best,
>>Ray
>>
>>Ray Luo wrote:
>>
>>
>>
>>>Hi Ross,
>>>
>>>Yes, this is a bug. I can reproduce the reported problem on an
>>>SGI/IRIX workstation. Fortunately, a oneline fix in "sa_driver.f"
>>>solves the problem. pbsa now passes all tests after the fix. After
>>>testing with ifort and g95, I'll check in the fix into Amber10 and
>>>upload a bugfix for both the pbsa and sander "sa_driver.f" tomorrow.
>>>
>>>Best,
>>>Ray
>>>
>>>
>>>Ross Walker wrote:
>>>
>>>
>>>
>>>>Hi All,
>>>>
>>>>Please see the message from Roberto below with regards to
>>>>
>>>>
>>problems in
>>
>>
>>>>Amber
>>>>9 on Irix and Altix. He has found a problem with an
>>>>
>>>>
>>algorithm in pbsa.
>>
>>
>>>>However, this exact same algorithm is used in
>>>>$AMBERHOME/src/sander/sa-driver.f,
>>>>
>>>>
>>$AMBERHOME/src/pbsa/sa-driver.f and
>>
>>
>>>>$AMBERHOME/src/pbsa/pb_sasa.f
>>>>
>>>>I suspect this is behind a number of problems we are
>>>>
>>>>
>>seeing with PB test
>>
>>
>>>>cases on various machines.
>>>>
>>>>Can anybody see what is wrong with the algorithm / see a
>>>>
>>>>
>>quick way to
>>
>>
>>>>fix
>>>>it?
>>>>
>>>>All the best
>>>>Ross
>>>>
>>>>
>>--
>>====================================================
>>Ray Luo, Ph.D.
>>Department of Molecular Biology and Biochemistry
>>University of California, Irvine, CA 92697-3900
>>Office: (949)824-9528 Lab: (949)824-9562
>>Fax: (949)824-8551 e-mail: rluo.uci.edu
>>Home page: http://rayl0.bio.uci.edu/rayl/
>>====================================================
>>
>>
>>
>>
>
>
>.
>
>
>
--
====================================================
Ray Luo, Ph.D.
Department of Molecular Biology and Biochemistry
University of California, Irvine, CA 92697-3900
Office: (949)824-9528 Lab: (949)824-9562
Fax: (949)824-8551 e-mail: rluo.uci.edu
Home page: http://rayl0.bio.uci.edu/rayl/
====================================================
Received on Wed May 03 2006 - 06:07:11 PDT
