> On Apr 28, 2017, at 6:49 PM, Adams, John E. <AdamsJE.missouri.edu> wrote:
>
> AND installing the binary distribution DOES produce correct tleap
> behavior.
Great. This is why we are trying hard to distribute binary AT too.
> I’m curious why compilation of the source code failed for
> tleap, though.
My guess: I look at config.h
-L/opt/local/lib/gcc49/gcc/x86_64-apple-darwin16/4.9.4/../../../ -lgfortran
So basically gfortran in GNU compiler distro here is used. (How do you install it?). Clang and GNU is not compatible.
We suggest user to use clang because macos natively support it, and the gfortran version suggested in amber website is compatible with clang.
You can try
otool -L bin/teLeap
for your and our binary AT too see how tleap is linked.
More guess: did you compile at16 with GNU compiler? (-gnu).
Hai
>
> John
> --
>
>> On 4/28/17, 5:24 PM, "Adams, John E." <AdamsJE.missouri.edu> wrote:
>>
>> I am using the fresh tar file. My config.h is attached.
>> --
>> On 4/28/17, 5:15 PM, "Hai Nguyen" <nhai.qn.gmail.com> wrote:
>>
>>
>>> If tleap tests did not pass, there is something wrong with compiling it.
>>>
>>> 1. How do you install AT17? (from upgrade or from a fresh tarfile?)
>>> - If you using "upgrade", did you "make distclean" to wipe
>>> previous install yet?
>>> 2. your compilers (even better to attache config.h here)
>>> 3. Sounds overkill (optional): You can to install our built to
>>> somewhere and try that tleap?
>>>
>>> http://ambermd.org/#AmberTools (check "Binary distribution" section)
>>>
>>> Hai
>>>
>>> On Fri, Apr 28, 2017 at 5:59 PM, Adams, John E. <AdamsJE.missouri.edu>
>>> wrote:
>>>> Hai,
>>>>
>>>> Attached is the entire set of files needed for leap. There ARE failed
>>>> tests involving leap (sorry that I missed them previously)‹a log file
>>>> with
>>>> the failed tests is included as well.
>>>>
>>>> John
>>>> --
>>>>
>>>>
>>>>> On 4/28/17, 1:55 PM, "Hai Nguyen" <nhai.qn.gmail.com> wrote:
>>>>>
>>>>> And does the amber test (e.g: tleap test) pass yet?
>>>>>
>>>>> Hai
>>>>>
>>>>>> On Fri, Apr 28, 2017 at 2:50 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:
>>>>>> is it possible to attach file(s) with exact command to reproduce
>>>>>> error
>>>>>> here?
>>>>>> thanks
>>>>>>
>>>>>> Hai
>>>>>>
>>>>>> On Fri, Apr 28, 2017 at 2:03 PM, Adams, John E.
>>>>>> <AdamsJE.missouri.edu>
>>>>>> wrote:
>>>>>>> Scott,
>>>>>>>
>>>>>>> If I run teLeap directly, I still get the Abort trap: 6 message just
>>>>>>> after the program tells me ³Building improper torsion parameters².
>>>>>>>
>>>>>>>
>>>>>>> On Apr 28, 2017, at 11:21 AM, Scott Brozell
>>>>>>> <sbrozell.rci.rutgers.edu<mailto:sbrozell.rci.rutgers.edu>> wrote:
>>>>>>>
>>>>>>> Hi,
>>>>>>>
>>>>>>> On Thu, Apr 27, 2017 at 03:45:51PM +0000, Adams, John E. wrote:
>>>>>>> I am constructing input for an organometallic zirconium compound
>>>>>>> using
>>>>>>> the procedure in Tutorial A20, specifically the MCPB.py branch of
>>>>>>> that
>>>>>>> tutorial. The system build was successful in AmberTools16 with the
>>>>>>> following tleap.in file.
>>>>>>>
>>>>>>> source oldff/leaprc.ff14SB
>>>>>>> source leaprc.gaff2
>>>>>>> addAtomTypes {
>>>>>>> { "M1" "Zr" "sp3" }
>>>>>>> { "Y1" "O" "sp3" }
>>>>>>> { "Y2" "O" "sp3" }
>>>>>>> { "Y3" "O" "sp3" }
>>>>>>> { "Y4" "O" "sp3" }
>>>>>>> { "Y5" "O" "sp3" }
>>>>>>> { "Y6" "O" "sp3" }
>>>>>>> { "Y7" "O" "sp3" }
>>>>>>> { "Y8" "O" "sp3" }
>>>>>>> }
>>>>>>> ZR1 = loadmol2 ZR1.mol2
>>>>>>> LG1 = loadmol2 LG1.mol2
>>>>>>> loadamberparams LIG.frcmod
>>>>>>> loadamberparams frcmod.ions1lm_126_tip3p
>>>>>>> loadamberparams ZRLIG_mcpbpy.frcmod
>>>>>>> mol = loadpdb ZRLIG_mcpbpy.pdb
>>>>>>> bond mol.1.ZR mol.2.O10
>>>>>>> bond mol.1.ZR mol.2.O11
>>>>>>> bond mol.1.ZR mol.2.O27
>>>>>>> bond mol.1.ZR mol.2.O28
>>>>>>> bond mol.1.ZR mol.2.O45
>>>>>>> bond mol.1.ZR mol.2.O46
>>>>>>> bond mol.1.ZR mol.2.O62
>>>>>>> bond mol.1.ZR mol.2.O63
>>>>>>> savepdb mol ZRLIG_dry.pdb
>>>>>>> saveamberparm mol ZRLIG_dry.prmtop ZRLIG_dry.inpcrd
>>>>>>> solvatebox mol TIP3PBOX 10.0
>>>>>>> addions mol Na+ 0
>>>>>>> addions mol Cl- 0
>>>>>>> savepdb mol ZRLIG_solv.pdb
>>>>>>> saveamberparm mol ZRLIG_solv.prmtop ZRLIG_solv.inpcrd
>>>>>>> quit
>>>>>>>
>>>>>>> (the file is written automatically by stage 4 of the MCPB.py
>>>>>>> procedure
>>>>>>> except for the addition of the line specifying gaff2).
>>>>>>>
>>>>>>> Running tleap with this file after the upgrade to AmberTools17 gives
>>>>>>> the following error message:
>>>>>>>
>>>>>>> /Users/JEAdams/amber16/bin/tleap: line 10: 765 Abort trap: 6
>>>>>>> $AMBERHOME/bin/teLeap -I$AMBERHOME/dat/leap/prep
>>>>>>> -I$AMBERHOME/dat/leap/lib -I$AMBERHOME/dat/leap/parm
>>>>>>> -I$AMBERHOME/dat/leap/cmd $*
>>>>>>>
>>>>>>> The leap.log file does not indicate a problem, but there is no entry
>>>>>>> after Building improper torsion parameters.
>>>>>>>
>>>>>>> I am running on MacOS v10.12.4.
>>>>>>>
>>>>>>> Hmm, I never seen that error before !
>>>>>>> There have only been 8 commits in AmberTools/src/leap in the last
>>>>>>> 400
>>>>>>> days.
>>>>>>> Only 1 looks suspicious.
>>>>>>>
>>>>>>> What happens if you run teLeap directly, ie:
>>>>>>>
>>>>>>> $AMBERHOME/bin/teLeap -I$AMBERHOME/dat/leap/prep
>>>>>>> -I$AMBERHOME/dat/leap/lib -I$AMBERHOME/dat/leap/parm
>>>>>>> -I$AMBERHOME/dat/leap/cmd bla bla
>>>>>>>
>>>>>>> scott
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> AMBER mailing list
>>>>>>> AMBER.ambermd.org<mailto:AMBER.ambermd.org>
>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>>>
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>>>>>
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>>>>
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Received on Fri Apr 28 2017 - 16:00:03 PDT
