AND installing the binary distribution DOES produce correct tleap
behavior. I’m curious why compilation of the source code failed for
tleap, though.
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
>>>>>>
>>>>>>
>>>>>> _______________________________________________
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>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>>
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Received on Fri Apr 28 2017 - 16:00:02 PDT
