Dear Amber users,
I am trying to parameterize a ligand using
Antechamber (included in Ambertools). When I use amber11 there is no
problem, but with Amber14, I got convergence problems:
$AMBERHOME/bin/antechamber -i ligand.pdb -fi pdb -o ligand.mol2 -fo mol2 -c bcc -s 2 -nc 0
Running: /opt/amber14//bin/bondtype -j full -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
Running: /opt/amber14//bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff
Total number of electrons: 516; net charge: 0
Running: /opt/amber14//bin/sqm -O -i sqm.in -o sqm.out
Error: cannot run "/opt/amber14//bin/sqm -O -i sqm.in -o sqm.out" of bcc() in charge.c properly, exit
If I look at the file sqm.out I can see that the error is related to convergence:
QMMM: ERROR!
QMMM: Unable to achieve self consistency to the tolerances specified
QMMM: No convergence in SCF after 1000 steps.
QMMM: E = -0.4533E+07 DeltaE = -0.4975E-09 DeltaP = 0.7039E-13
QMMM: Smallest DeltaE = 0.1737E-09 DeltaP = 0.6051E-07 Step = 105
When
I do exactly the same, but using amber11 the calculation finishes
without problem. Anyway, I have tried to minimize the ligand structure,
but the problem appears again.
How could I solve the problem? Is
there any way to decrease the convergence criteria in sqm but directly
from the line $AMBERHOME/bin/antechamber -i ligand.pdb -fi pdb -o
ligand.mol2 -fo mol2 -c bcc -s 2 -nc 0?
Thanks a lot for your help in advance.
Best wishes,
Rebeca.
Dr. Rebeca Garcia
Santiago de Compostela University
Spain
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Received on Mon Dec 29 2014 - 05:30:03 PST
