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 “Building improper torsion parameters”.
>>
>>
>> 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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Received on Fri Apr 28 2017 - 12:00:03 PDT
