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.
I would appreciate any help you can provide in diagnosing the problem.
Thanks,
John Adams
--
John E. Adams, PhD
Curators’ Distinguished Teaching Professor Emeritus
Department of Chemistry
University of Missouri
Columbia, MO 65211-7600
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Received on Thu Apr 27 2017 - 09:00:02 PDT
