Dear Amber experts,
I have on my server AMBER16 and AMBER TOOLS16.
The ligand MS75 in my protein-ligand complex needs previous parametrisation by ANTECHAMBER.
The MS75 ligand has a total charge -1.
Applying original MOPAC2016 with AM1 hamiltonian I have calculated the MS75
without any problem.
Unfortunately, the standard AMBER command line:
antechamber -i MS75.pdb -fi pdb -o MS75.mol2 -fo mol2 -c bcc -s 2
returns with error message because the input MS75.pdb was incorrectly interpreted as having charge=0
Running: /var/spool/scratch/shokhen/amber16/bin/bondtype -j full -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
Running: /var/spool/scratch/shokhen/amber16/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff
Total number of electrons: 231; net charge: 0
INFO: Number of electrons is odd: 231
Please check the total charge (-nc flag) and spin multiplicity (-m flag)
Running: /var/spool/scratch/shokhen/amber16/bin/sqm -O -i sqm.in -o sqm.out
Error: cannot run "/var/spool/scratch/shokhen/amber16/bin/sqm -O -i sqm.in -o sqm.out" of bcc() in charge.c properly, exit
The top of smq.in file automatically generated by bcc parameter in the antechamber command line
demonstrates incorrect molecular charge definition based on input coordinates of the MS75.pdb:
Run semi-empirical minimization
&qmmm
qm_theory='AM1', grms_tol=0.0005,
scfconv=1.d-10, qmcharge=0,
Could somebody advise me how to modify the command line
antechamber -i MS75.pdb -fi pdb -o MS75.mol2 -fo mol2 -c bcc -s 2
in order to setup the charge=-1 for MS75 ligand?
Thank you,
Michael
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Received on Thu Jul 13 2017 - 02:30:03 PDT
