Hello all,
Sorry if I ask the following questions in this forum.
I just developed the LAMMPS data file for benzaldehyde phenylhydrazone using TopoTools, as shown below. Each partial charge is calculated by involving the electrovalency, electronegativity, both number of bonding and non-bonding electron. I am wondering if that is the way to calculate the charge as in TopoTools.
Subsequently, I try to find out the force field parameter, such as pair_coeff, bond_coeff, angle_coeff, dihedral_coeff, improper_coeff from http://zarbi.chem.yale.edu/ligpargen/. However, the number of dihedral types and improper types are different from those generated by TopoTools.
Any suggestion would be appreciated.
set selh [atomselect top {name H}]
$selh set mass 1.00800
$selh set charge 0.064
set selc [atomselect top {name C}]
$selc set mass 12.01100
$selc set charge -0.064 ;
set seln [atomselect top {name N}]
$seln set mass 14.0067
$seln set charge -0.205 ;
$selh delete
set selh [atomselect top {index 10}]
$selh set charge 0.165 ; #H1
$selc delete
set selc [atomselect top {index 5}]
$selc set charge 0 ; #C6
$selc delete
set selc [atomselect top {index 6}]
$selc set charge 0.141 ; #C7
$selc delete
set selc [atomselect top {index 9}]
$selc set charge 0.102 ; #C8
$seln delete
set seln [atomselect top {index 8}]
$seln set charge -0.267 ; #N2
set sel [atomselect top all]
topo retypebonds
topo numbondtypes
topo guessangles
topo numangletypes
topo guessdihedrals
topo numdihedraltypes
topo guessimpropers
topo numimpropertypes
mol reanalyze top
set minmax [measure minmax $sel -withradii]
set box [vecscale 1.1 [vecsub [lindex $minmax 1] [lindex $minmax 0]]]
pbc set $box
set center [measure center $sel weight none]
$sel moveby [vecscale -1.0 $center]
TopoTools::replicatemol top 3 3 4
topo writelammpsdata data.BDHP full
animate write pdb BDHP.pdb
Regards,
Rizal