Re: [AMBER] tleap input file that fails following upgrade to AmberTools17

From: Adams, John E. <AdamsJE.missouri.edu>
Date: Fri, 28 Apr 2017 21:59:15 +0000

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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Received on Fri Apr 28 2017 - 15:00:03 PDT