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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>>>>
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>>
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Received on Fri Apr 28 2017 - 15:30:03 PDT
