- You can use the following LEaP script to define the FF atom types:
NH4 = loadmol2 Mol_m1-o1.mol2
set NH4 name "NH4"
# head & tail not needed since whole molecule
# connect0 & connect1 not needed since whole molecule
set NH4.1 restype solvent
set NH4.1 name "NH4"
# set FF atom types
set NH4.1.N1 type N3
set NH4.1.H11 type H
set NH4.1.H12 type H
set NH4.1.H13 type H
set NH4.1.H14 type H
# See http://q4md-forcefieldtools.org/Tutorial/leap-mol2.php
savemol2 NH4 Mol_m1-o1-bis.mol2 1
- no missing force field parameter should be found by LEaP
regards, Francois
PS
There is a rounding off error of 2.10-4 e in the mol2 file generated
by R.E.D. IV; you might use the "Re_fit" mode of R.E.D. III.51 and set
$COR_CHR = "5" to make this error = 0.
See http://q4md-forcefieldtools.org/RED/HowTo-III.5.pdf page 6.
# charge values at 1.10-4 e
> NH4 = loadmol2 Mol_m1-o1.mol2
Loading Mol2 file: ./Mol_m1-o1.mol2
Reading MOLECULE named NH4
> charge NH4
Total unperturbed charge: 0.999800
Total perturbed charge: 0.999800
# charge values at 1.10-5 e
> NH4 = loadmol2 Mol_m1-o1.mol2
Loading Mol2 file: ./Mol_m1-o1.mol2
Reading MOLECULE named NH4
> charge NH4
Total unperturbed charge: 1.000000
Total perturbed charge: 1.000000
