Eew947: Created page with "=Introduction/Motivation= * GDMA has issues/difficulties with SP calculations of higher basis sets. =What you need= # FCHK file # GDMA output file # Example of input files of para-cresol is available at /home/wuch/work/research/ligand_param/sample/pot/tutorial Image:Cresol.png =Process= Follow AMOEBA Ligand Param Instructions to get output from GDMA Generate multipoles in Tinker format (gdout.xyz and gdout..."

2025-04-21T23:26:54Z

Created page with "=Introduction/Motivation= * GDMA has issues/difficulties with SP calculations of higher basis sets. =What you need= # FCHK file # GDMA output file # Example of input files of para-cresol is available at /home/wuch/work/research/ligand_param/sample/pot/tutorial Image:Cresol.png =Process= *Follow AMOEBA Ligand Param Instructions to get output from GDMA *Generate multipoles in Tinker format (gdout.xyz and gdout..."

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=Introduction/Motivation=
* GDMA has issues/difficulties with SP calculations of higher basis sets.

=What you need=
# FCHK file
# GDMA output file
# Example of input files of para-cresol is available at /home/wuch/work/research/ligand_param/sample/pot/tutorial

[[Image:Cresol.png]]

=Process=

*[[Research:Amoeba_ligand_par#Multipoles_calculation.|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

Research:Potential Tutorial - Revision history