Documentation is hosted at http://parmhess.readthedocs.io.
This master branch is not up to date. Head to https://github.com/ruixingw/tsubasa/releases.
Tsubasa is a program to prepare input files for Hessian Fitting parameterization.
Hessian Fitting scheme requires QM optimized geometry, Hessian, RESP charge, and a MM input file. Preparing MM input file for Hessian Fitting is a very complicated work for human. Tsubasa program automatically do all calculations, identify MM functions and format every thing done into a MM input file, which is eventually used by Hessian Fitting programs.
Tsubasa requires the following packages.
- Clone this repository by
git clone https://github.com/ruixingw/tsubasa.git. - Make
tsubasa.pyglobal approachable. (You can 1. add thetsubasadirectory to your $PATH environment, or 2. create a soft link for tsubasa.py in your existing $PATH.).
An example of benzene (C6H6) is shown here.
- Prepare Input file including geometry and connectivity.
The input file can be easily prepared by GaussView and deleting some lines. The format is as followed.
0 1
C -0.196066032299 0.083954610270 0.000060359368
C 1.202825076336 0.083884471006 0.000506018868
C 1.902331654047 1.295325035437 -0.000047136416
C 1.202946707718 2.506835148041 -0.001045596240
C -0.195944409385 2.506905316939 -0.001491091778
C -0.895450997150 1.295464738220 -0.000938299116
H -0.739751345816 -0.857625934164 0.000489987063
H 1.746416421211 -0.857750015636 0.001281451623
H 2.989606822804 1.295270625436 0.000299297106
H 1.746632277886 3.448415533193 -0.001475037473
H -0.739536124154 3.448539598789 -0.002266379146
H -1.982726171199 1.295519560979 -0.001284573853
1 2 1.5 6 1.5 7 1.0
2 3 1.5 8 1.0
3 4 1.5 9 1.0
4 5 1.5 10 1.0
5 6 1.5 11 1.0
6 12 1.0
7
8
9
10
11
12
Note that there is a blank line at the end. Save this file with a ".gau" extension, for example, "ben.gau".
-
Run "tsubasa.py". A config file will be copied to the current folder and named as "ben.yml".
-
Modify the config file according to your own needs. The config file includes the commands for Gaussian. Usually, it is already good to use. Here, we do not edit anything.
-
Run "tsubasa.py" again. Program will now automatically perform Optimization, Frequency calculation, RESP calculation, and identify the internal coordinates and MM functions, and finally prepare MM input file. Files are saved in "tsubasa" folder.
ruixingw@boonlay-ntu test $ ls
freqben.fchk freqben.log input.inp mmben.com tsubasa/
ruixingw@boonlay-ntu test $ cd tsubasa
ben.yml ben.tsubasa freqben.com freqben.log mmben.com optben.com respben.mol2 respben.com
ben.gau freqben.chk freqben.fchk input.inp optben.chk optben.log respben.chk respben.log
The mmben.com and freqben.fchk is then used to perform Hessian Fitting job. freqben.log is used to evaluate the performance (L1 Norm of frequencies). input.inp includes internal coordinates information but is not used.
The content of mmben.com is as follow.
%mem=12gb
#p amber=softonly geom=connectivity nosymm
iop(4/33=3,7/33=1)
freq
MM-name
0 1
C-ca--0.117738 -0.196066032299 0.083954610270 0.000060359368
C-ca--0.117738 1.202825076336 0.083884471006 0.000506018868
C-ca--0.117738 1.902331654047 1.295325035437 -0.000047136416
C-ca--0.117738 1.202946707718 2.506835148041 -0.001045596240
C-ca--0.117738 -0.195944409385 2.506905316939 -0.001491091778
C-ca--0.117738 -0.895450997150 1.295464738220 -0.000938299116
H-ha-0.117738 -0.739751345816 -0.857625934164 0.000489987063
H-ha-0.117738 1.746416421211 -0.857750015636 0.001281451623
H-ha-0.117738 2.989606822804 1.295270625436 0.000299297106
H-ha-0.117738 1.746632277886 3.448415533193 -0.001475037473
H-ha-0.117738 -0.739536124154 3.448539598789 -0.002266379146
H-ha-0.117738 -1.982726171199 1.295519560979 -0.001284573853
1 2 1.5 6 1.5 7 1.0
2 3 1.5 8 1.0
3 4 1.5 9 1.0
4 5 1.5 10 1.0
5 6 1.5 11 1.0
6 12 1.0
7
8
9
10
11
12
AmbTrs ca ca ca ca 0 180 0 0 0.0 XXXXXX 0.0 0.0 1.0
AmbTrs ha ca ca ca 0 180 0 0 0.0 XXXXXX 0.0 0.0 1.0
AmbTrs ha ca ca ha 0 180 0 0 0.0 XXXXXX 0.0 0.0 1.0
HrmBnd1 ca ca ha XXXXXX 120.0000
HrmBnd1 ca ca ca XXXXXX 120.0000
HrmStr1 ca ha XXXXXX 1.08728
HrmStr1 ca ca XXXXXX 1.39889
Nonbon 3 1 0 0 0.0 0.0 0.5 0.0 0.0 -1.2
VDW ca 1.9080 0.0860
VDW ha 1.4590 0.0150
- The dihedrals are separately idenfied and they are temporarily assigned n=2, phase=180 degree and NPaths=1.0. Usually, wildcards is used to represent a set of dihedrals, and one must manually edit it.
AmbTrs * ca ca * 0 180 0 0 0.0 XXXXXX 0.0 0.0 4.0
- You are ready for parameterization. Go ahead to Parmhess.
For other options, please see the Tsubasa Reference Manual.