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The external webpage that describes the usage of [http://water.bme.utexas.edu/wiki/index.php/Software:autoparm poltype.py] is on water.

== Issues/Feature Requests ==

*Add pi-tors term to NH2 (i.e. propanamide)
**Adenine example http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=190
*Default opbendunit to TINKER 5 format
**[[Talk:Logs:parameterization]]
**Add opbend v4 option
*Add biotypes to parameters
*Issues with [http://water.bme.utexas.edu/wiki/index.php/Software:autoparm2 1P1O]

=== OP Bend ===

*Differences between the opbend terms from poltype and amides from amoeba '09 parameters
*Main difference is for CO - N
*First number is from poltype. Numbers in parantheses are from AMOEBA '09 small molecules and AMOEBA_BIO '09)

# CH3 CO
opbend 401 403 0 0 14.402 (same, N/A)
# CO N
opbend 403 404 0 0 71.940 (12.9, 70.5)
# N CO
opbend 404 403 0 0 107.910 (same, same)
# O CO
opbend 407 403 0 0 122.298 (46.8, 54.0)
# H N
opbend 408 404 0 0 5.755 ( 5.8, 12.9)

=== Updated polarizabilities ===

The third column is polarizablity; and the fourth one is vdW, if different with current amoeba. 

{| cellspacing="1" cellpadding="1" border="1" width="60%"
|-
| 
| O- (in COO-) 
| 1.600 
| 3.700/0.1290 
|-
| 
| S- (in R-S-) 
| 4.000 
| 4.200/0.3550 
|-
| 
| N(aromatic HIS) 
| 1.500 
| 
|-
| 
| C(aromatic HIS & COO-) 
| 1.750 
| 
|-
| 
| H(aromatic HIS) 
| 0.696 
| 
|}

 

==Parameterization==
*Bisector: set XZ component of quadrupole to 0
*Use parameters from /home/pren/AMOEBA
**amoeba_v2_new.prm
**amoeba_2009_ver4.prm.isoprop
*If all opbend angles for atom X of minimized structure > 4 degrees, remove opbend parameters and set equilibrium angles around atom to 110 degrees
**Confirm with Jenny if "4 degrees" and "110 degrees" are correct.
*Set opbend force constant according to amoeba.prm
**1.7 for carbonyl C=O, C-C(O), and -N-C=O (amide)
**~0.6-0.7 for alkane C?
**Add opbend to nitromethane-like groups
*Remove pi-torsion param for C-C=C-C and increase torsion to 5.5 from 4.5
*quadrupole scaling on OH in alcohol (-Csp3-OH)
**Use [http://water.bme.utexas.edu/wiki/index.php/Software:parmnote#GDMA_input GDMA Input]
**Scale by 70% if gdma v2.2 procedure is used
**Scale by 60% if gdma v1.2 or 1.3 is used (switch=0 and H radius 0.65)
*Classify terminal atoms that are the same element together
**Check Gaussian MBO (bond order to get accurate valence info)
*Torsion
**Minimize with HF/6-31G8 or M06L
**SP using DFT with ML06 functional (in G09)
**Methyl group torsion 0.299
**Only single bonds with heavy atoms
*Plot phase angle without torsion parameters
*DFT vs HF optimization? Which is better?
*Modify polarizability for imidazole N and C (based on Jenny's findings)
*New functional groups
**fit_struct (run with MP2/6-31++G(2d,2p)
***bond, angle, opbend
**polarizability (pol-eps = 0.000001)
**vdw (compare distance, dimer/interaction energy)
***To calculate dimer energy from Gaussian output:
****BSSE Corrected Dimer energy = (1 - 2 - 3) * 621.5095 # Constant to convert HF to kcal/mol
****Non-BSSE Corrected Dimer energy = (1 - 4 - 5) * 621.5095
****Values 1, 2, 3, 4, 5 are taken by grepping EUMP2 from Gaussian logfile
****Take the EUMP2 values from the 5 lines
****Compare BSSE corrected and non-corrected
****Try to get somewhere in between
*Add option for Freq for DMA QM
*Fix QM torsion for all heavy atoms
*Generate torsion conformations with AMOEBA rather than QM (add option)

===Status===
*What value to use for alkane? 0.6 or 0.7?
*Question: Amide opbend values don't match.
**/home/pren/AMOEBA/amoeba_v2_new.prm
**Values we discussed 1.7

==Validation==
*Calculate molecular polarizability: B3LYP/6-311++G(2d,2p)
*Water-compound Dimer Energy
**Opt: MP2/6-31++G(2d,2p)
**SP: MP2/aug-cc-pVTZ & Counterpoise 1,1,1,1,1,1 (using Q-chem/RI TRIM)
**Use to modify some vdW parameters
**nitro - water: find O -- H distance, and angle
*Run QM of nitro as N-O bond distance changes
**Explore changes in multipoles
*Run QM with Q-Chem (rimp2)

=Bugs/Feature request=
*Convert Tinker 5 to Tinker 4

=Paper #1=
==Method==
*Parametrization: Run HF/6-31G* opt, single point MP2/6-311G** -> GDMA (polgrp, average/symm) -> ESP of  MP2/6-311++G(2d2p)
*Assign all other valence, vdw, polarizability, ...
*High-level QM data for dimers/complexes (RI-MP2/aug-cc-pvtz -pvdz)

==Results==
===DFT vs. MP2===
*Molecule/water dimer energy
*Torsion energy
*Geometry?
*(w/ ~10-20 molecules)
===AMOEBA vs. DFT===
*Based on DFT vs. MP2 findings
====Monomer====
*Vibrational frequency
*Dipole moment (using different conformations)
*ESP
*Geometry (RMSD)
====Hetero Dimer w/ water====
*Energy
*Structure
*QM:MP/6-31+G* opt and MP2/aug-cc-pvtz for dimerization energy all the *other (validation): DFT/B3LYP 6-31G* opt and dimer energy
*Correlation w/ solvation energy

===Solvation Free Energy===
*Choose 5/20 molecules which should agree with fixed-charge FF and some that should showcase strenght of AMOEBA FF.

=Done=
*Implement symmetry class assignment in Python
*Implement atom type assignment based on SMARTS string
*Implemented opbend framework ([[User:Jwu|Jwu]] 05:05, 29 June 2010 (UTC))
**Added opbend values from amoeba_v2_new.prm ([[User:Jwu|Jwu]] 22:09, 9 July 2010 (UTC))
**Re-implemented opbend to use values ([[User:Jwu|Jwu]] 22:10, 6 July 2010 (UTC))
*Match polarization group class ID with multipole class IDs
*print/check bond, angle and torsion deviations ([[User:Jwu|Jwu]] 03:58, 12 March 2010 (UTC))
*select ~ 200 molecules
*From Rizzo Supplementary Info:
*#1040
*#1014
*#1018
*#1019
*Describe Babel instructions ([[User:Jwu|Jwu]] 22:31, 9 March 2010 (UTC))
*Remove duplicate multipoles ([[User:Jwu|Jwu]] 22:33, 10 March 2010 (UTC))
*Geometry: RMSD AMOEBA vs. QM ([[User:Jwu|Jwu]] 03:57, 12 March 2010 (UTC))
*Check polarization groups ([[User:Jwu|Jwu]] 07:40, 12 March 2010 (UTC))
**Alcohol (-C-OH)
**(-C-NH2)
**Benzene ring w/ CH2 (-CH2-c1ccccc1)
**Phenol (-c1ccccc1(-OH)
**(-CH2-C(=O)-NH2)
*Check electrostatics ([[User:Jwu|Jwu]] 20:25, 12 March 2010 (UTC))
**net charges (0 or -1, +1...)
**dipole and quadrupole
**ESP
*minimize your molecule and compare to the Qm structure. RMSD should be small ([[User:Jwu|Jwu]] 20:25, 12 March 2010 (UTC))
*Run QM for set of molecules ([[User:Jwu|Jwu]] 16:41, 17 March 2010 (UTC))
**Copy correct SDF files and generate load-balanced scripts to run QM
**Modify poltype to run QM only ([[User:Jwu|Jwu]] 20:20, 15 March 2010 (UTC))
**Install babel 2.2.3 and python bindings on TI3d cluster (ddfe) ([[User:Jwu|Jwu]] 20:20, 15 March 2010 (UTC))
*QM method ([[User:Jwu|Jwu]] 21:01, 21 June 2010 (UTC))
**Perform GDMA on MP2/6-311G** to get charge
**minimize ESP RMSD to MP2/6-311++G(2d,2p) (or Aug-CC-pVTZ) to get dipole, quadropole
*Check for amide (OCN), acetic (OCC) to recognize polarization groups
*Scale amine quadrupoles ([[User:Jwu|Jwu]] 03:51, 1 December 2011 (UTC))
*Use ESP convergence (0.5) ([[User:Jwu|Jwu]] 03:51, 1 December 2011 (UTC))
*Polarization group of functional group should include adjacent SP3 carbon ([[User:Jwu|Jwu]] 03:51, 1 December 2011 (UTC))
*Explain how aromatic carbons are found in Babel on water site ([[User:Jwu|Jwu]] 04:51, 1 December 2011 (UTC))
*Explain how charge multiplicity can be changed in SDF file on water site ([[User:Jwu|Jwu]] 04:51, 1 December 2011 (UTC))
*Explain in docs, what are from database (and how it can be expanded), and what will be computed. ([[User:Jwu|Jwu]] 05:07, 1 December 2011 (UTC))
**How are bond orders determined
***single vs double bonds
***aromatic C
***What are aromatic C information for?

=Notes/Misc.=
*In amoebapro4.prm, header “opbendunit 0.02191418”, so actual force constant is “smaller” than amobeabiov4.prm
*amobeabiov4.prm (doesn’t have the opbendunit in the header)
**Uses the default: 1/radian^2, where radian =57.29
**opbend_force_in_prm= actual_opbend_force_used* (radian**2/opbunit)
**opbendunit is 0.02191418 instead of 1/57.3^2 (when not defined the opbendunit in the header)
**Force constant in prm should be smaller by 71.9
**Can’t mix parameters from the amoebapro4.prm and amoebbiov4.prm right now
**amber handles amoebapro4.prm correctly, but need to check the amobeabiov4.prm

==Paper #2==
Solvation
*HFE energy >50 molecules?
*Solvation energy too negative
**23 dimethylpyridine
**NN dimethylformamide
**diisopropylamine
**4 methoxyacetophenone
**2 ethoxyethanol
**propanone
***Test with ethanone?
**Notes in Dropbox:small_mol_johnny\solvation\solv-free-energy.xls

==Paper #3, etc.==
Solvation with octane (LogP)

=Links=
*[[Research:Typer]]
*[http://water.bme.utexas.edu/wiki/index.php/Software:parmnote Notes on parameterization]
*[http://water.bme.utexas.edu/wiki/index.php/Software:autoparm2 Jenny's notes on parameterization]

Logs:parameterization - Revision history

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