Re: [AMBER-Developers] significant recent tleap changes

From: Yong Duan <>
Date: Fri, 11 Nov 2011 19:16:20 -0800

Can you send the older version code to me? Or, perhaps in the released
AMBER 11 tree?

OK, I stop checking the codes. Sorry! My bad.


On 11/11/11 3:55 PM, "Ross Walker" <> wrote:

>Hi Yong,
>> Improper 1-4's are never used, either in sander or in pmemd. I am not
>> sure
>> in other programs, hopefully consistent. Putting 0's is fine. I can
>> update
>> that.
>What you mean is 1-4 impropers do not feature in the code that calculates
>1-4 VDW and EEL I assume? - Certainly they are used in the dihedral code.
>Note the 0's should NOT just be there for the impropers. They should be
>there for ALL additional dihedrals. This is a safety check. The code
>only calculate a 1-4VDW / EEL for the first dihedral in a set it gets to.
>Having the additional dihedrals have scaling factors of 0 means if someone
>messes with things, and puts dihedrals out of order, messes up the section
>that labels unique dihedrals etc then you get infinity and the code
>rather than just silently producing junk.
>Thus I would make sure things match properly here with older code.
>> Besides these "failures", you will also see CMAP-related failures. Both
>> sander and pmemd can take CMAP without CHARMM option.
>Why have all the test cases not been updated along with the checkin???
>> This means the test suite needs to be updated and that the "new" test
>> suite will cause a lot of "failures" to the old code and vice versa.
>I always assume updating the test cases (not just replacing the saved
>but replacing them with results you know to be correct and have carefully
>tested by hand) is a key part of checking in updated code. If you don't
>include test cases and updated test cases with your code checkins then the
>code should NOT be being checked in.
>Note, once I have cruise control up and running properly running all the
>test cases on a regular basis if you check something in that breaks the
>you will be getting regular emails from the git server politely informing
>you of your 'mistake'.
>All the best
>|\oss Walker
>| Assistant Research Professor |
>| San Diego Supercomputer Center |
>| Adjunct Assistant Professor |
>| Dept. of Chemistry and Biochemistry |
>| University of California San Diego |
>| NVIDIA Fellow |
>| | |
>| Tel: +1 858 822 0854 | EMail:- |
>Note: Electronic Mail is not secure, has no guarantee of delivery, may not
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Received on Fri Nov 11 2011 - 19:30:03 PST
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