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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- application/octet-stream attachment: config.h
Received on Fri Apr 28 2017 - 15:30:04 PDT
