Research:Potential Tutorial

Introduction/Motivation

• GDMA has issues/difficulties with SP calculations of higher basis sets.

What you need

1. FCHK file
2. GDMA output file
3. Example of input files of para-cresol is available at /home/wuch/work/research/ligand_param/sample/pot/tutorial

Process

• Follow AMOEBA Ligand Param Instructions to get output from GDMA

• Generate multipoles in Tinker format (gdout.xyz and gdout.key)

/home/pren/tinker5-2-2009/source/poledit.x 1 gdout

• Poledit can be used to extract intramolecular polarization.
  • Needed to average multipoles of molecules with different conformations.

• Answer the following prompts

Enter Altered Local Frame Definition [<CR>=Exit] : 12 13 14
Enter Altered Local Frame Definition [<CR>=Exit] :
Enter Atom Number & Polarizability Values [<CR>=Exit] :
Enter a Bond between Polarization Groups [<CR>=Exit] :
Average the Multipoles of Equivalent Hydrogen Atoms [N] :  Y
Remove Y-Component Multipoles at Achiral Sites [N] :  Y 

• Better yet, create a file (poledit.input) with the responses (and appropriate carriage returns)

/home/pren/tinker5-2009-6/source/poledit.x 1 gdout < poledit.input

• Average multipoles of the same type

/home/wuch/work/research/ligand_param/dev/avgmpoles.pl gdout.key \
  gdout.xyz types.txt 1 16 21 gdout.key_2 gdout.xyz_2

• Prepend this to the newest key file (gdout.key_2)

parameters none
bondterm none
angleterm none
torsionterm none
vdwterm none
fix-monopole
potential-offset 1.0 #???

• Create grid points for molecule (gdout.grid and gdout.pot)

/home/pren/tinker5-2009-6/source/potential.x 2 gdout.xyz_2 Y

• Compute electrostatic potential from Total MP2 Density (gdout.cube)

/opt/g03/bin/cubegen 0 potential=MP2 cresolxyzsp.fchk gdout.cube -5 h < gdout.grid

• Create potential file for grid points readable by potential.x (gdout_cube.qmpot)

/home/pren/CHUANJIE/potcon/readcube/readcube gdout.cube

• Fit Electrostatic Parameters to Target Grid (gdout.key_3)

/home/pren/tinker5-2009-6/source/potential.x 5 gdout.xyz_2 gdout_cube.qmpot

• Append fitted multipoles to original parameter file

cat gdout.key_2 gdout.key_3 > gdout.key_4

• Modify class type in parameter file accordingly

Keywords for potential.x

• POTENTIAL-ATOMS: a list of the atoms whose potential grid points will be included in the potential fitting
  • use the usual TINKER mechanism where a negative number is the start of a range through the following atom number
  • For example "POTENTIAL-ATOMS -1 5 7 9" == 1-5, 7, 9
• POTENTIAL-FIT: a list of atoms whose electrostatic parameter values will be allowed to vary in the potential fitting
  • a negative number is the start of a range through the following atom number
• FIX-MONOPOLE: Do not fit for monopole (charges)
• FIX-DIPOLE: Do not fit for dipoles
• FIX-QUADRUPOLE: Do not fit for quadrupoles
• TARGET-DIPOLE: Fit for dipoles
• TARGET-QUADRUPOLE: Fit for quadrupoles
• POTENTIAL-SHELLS:
• POTENTIAL-SPACING:
• POTENTIAL-OFFSET:

2011 Dec example used for AMOEBAPRO 2.0

parameters ../../../parm/amoebapro5his2010.prm
bondterm none
angleterm none
torsionterm none
polar-eps 0.00001
fix-monopole 
POTENTIAL-OFFSET 1.0
POTENTIAL-SHELLS 5
POTENTIAL-SPACING 0.35
POTENTIAL-FIT -13 30

From /home/yues/amoebapro/multipole/TRP