4.4. Example: Pincer and Water Using topgen and Multiwfn
Tip
The sample input and output files can be found in testfiles/rigidmol/4-pincerwater.
In this section, we want to consider the cluster of a large molecular “pincer” and 13 water. For water, we can just use tip4p.xyz as done before. The pincer is shown below:
pincer.xyz
98
pincer
O 0.97308000 4.02950000 0.02172960
O 5.22818000 4.29840000 0.55213100
O 5.45578000 2.88710000 -1.50102000
H 5.65508000 3.42840000 -0.65915200
O 1.63082000 1.39760000 -3.81621000
H 0.64178000 1.28790000 -3.63132000
O -0.85420000 1.13280000 -3.02372000
O -3.63480000 3.01800000 0.37844100
O 0.94203000 -4.12400000 -0.01164950
O 5.22756000 -4.12300000 -0.19236000
O 5.19975000 -2.75900000 1.90677000
H 5.49911000 -3.28700000 1.08741000
O 1.10372000 -1.43100000 3.83101000
H 0.13381000 -1.37300000 3.54797000
O -1.31340000 -1.31100000 2.81292000
O -3.65480000 -3.37200000 -0.81056300
N -4.55230000 1.09440000 -0.99695900
H -4.54060000 1.90820000 -0.33085600
N -4.76650000 -1.44200000 0.39144300
H -4.65210000 -2.26500000 -0.25439400
C 1.94344000 3.43050000 -0.80416400
C 3.32617000 3.54260000 -0.60306300
C 4.12217000 2.86750000 -1.60098000
C 3.56742000 2.16740000 -2.68707000
C 2.17005000 2.08920000 -2.79643000
C 1.35713000 2.72410000 -1.83511000
C -0.12610000 3.02720000 -1.80688000
C -1.12760000 1.90760000 -2.07830000
C -2.35500000 1.91710000 -1.32846000
C -2.54310000 2.90300000 -0.24390400
C -1.40410000 3.67780000 0.23983600
H -1.50880000 4.16770000 1.20107000
C -0.25120000 3.62020000 -0.44329800
C 3.98051000 4.29050000 0.46425400
C 3.18432000 5.08190000 1.47209000
H 3.87937000 5.54190000 2.17506000
H 2.48025000 4.43970000 2.00742000
H 2.58977000 5.85330000 0.97167700
C 4.46758000 1.52720000 -3.70897000
H 5.36536000 1.12230000 -3.23581000
H 4.80242000 2.26570000 -4.44793000
H 3.93826000 0.73680000 -4.24433000
C -0.45280000 4.13300000 -2.87362000
H -1.49930000 4.43910000 -2.78952000
H -0.26720000 3.72570000 -3.87041000
H 0.19468000 4.99770000 -2.70998000
C -3.38270000 0.95820000 -1.61680000
C -3.16450000 -0.17800000 -2.56830000
H -3.99600000 -0.88000000 -2.56379000
H -2.24950000 -0.71000000 -2.30253000
H -3.00750000 0.20520000 -3.58020000
C -5.75190000 0.27390000 -1.07838000
H -5.66800000 -0.41200000 -1.92466000
C -6.98160000 1.17200000 -1.28347000
H -7.04050000 1.88830000 -0.45262600
H -6.84510000 1.75430000 -2.20072000
C -8.26660000 0.33820000 -1.34828000
H -8.23510000 -0.30800000 -2.23605000
H -9.12970000 1.00130000 -1.46934000
C 1.79603000 -3.47200000 0.89376900
C 3.19591000 -3.51400000 0.81872300
C 3.86255000 -2.79400000 1.87848000
C 3.17612000 -2.10600000 2.89516000
C 1.76972000 -2.10300000 2.87705000
C 1.08107000 -2.79400000 1.86047000
C -0.37560000 -3.18400000 1.70563000
C -1.45940000 -2.12200000 1.86764000
C -2.61180000 -2.20900000 1.01188000
C -2.63740000 -3.19800000 -0.08655830
C -1.41550000 -3.90500000 -0.45472100
H -1.39180000 -4.38300000 -1.42651000
C -0.34400000 -3.78600000 0.33979400
C 3.97534000 -4.19500000 -0.20265100
C 3.31726000 -5.00200000 -1.29460000
H 4.09514000 -5.37900000 -1.95885000
H 2.60358000 -4.39700000 -1.86056000
H 2.75164000 -5.83600000 -0.86495000
C 3.94193000 -1.40900000 3.98735000
H 4.83366000 -0.92100000 3.58815000
H 4.27651000 -2.12900000 4.74422000
H 3.30842000 -0.67200000 4.48277000
C -0.73050000 -4.29800000 2.75283000
H -0.65690000 -3.87500000 3.75749000
H -0.02310000 -5.12500000 2.65752000
H -1.74630000 -4.66500000 2.58197000
C -3.69130000 -1.28100000 1.15965000
C -3.63830000 -0.14400000 2.13635000
H -4.52880000 0.47930000 2.09032000
H -2.76620000 0.47890000 1.93537000
H -3.50560000 -0.52900000 3.14983000
C -5.91880000 -0.57300000 0.21221300
H -6.00050000 0.11350000 1.05878000
C -7.19980000 -1.41500000 0.12954700
H -7.29880000 -1.99900000 1.05068000
H -7.10010000 -2.13200000 -0.69707000
C -8.42930000 -0.52700000 -0.09348310
H -9.32510000 -1.15200000 -0.17414200
H -8.57210000 0.12090000 0.78154800
4.4.1. Calculate Parameters
First, we will use topgen to generate most information:
$ topgen pincer.xyz
You will get the following output:
Analyze topology for the molecule from "pincer.xyz" ... done.
Exporting results to "pincer" +
.gjf: GJF file with bonding information.
-cycles.txt: Containing cycle texts that can be used for ABCluster:geom calculation.
-bonding.xyz: XYZ file with bonding information for ABCluster:geom calculation.
-rigid.xyz: XYZ file with bonding information for ABCluster:rigidmol calculation.
.psf: PSF file with topology informaition for ABCluster:geom/NAMD calculations.
In "pincer-rigid.xyz" and "pincer.psf":
"X" means unknown atomic type.
Total charge: 1.8360
In pincer.psf and pincer-rigid.xyz, the topology and Lennard-Jones parameters have been automatically generated. The atom typing is done using graph representation learning. Please refer to:
Tip
Zhang, J. Atom Typing Using Graph Representation Learning: How Do Models Learn Chemistry? J. Chem. Phys. 2022, 156, 204108.
However, the charge is 1.8360, which is wrong. To obtain a reasonable charges, we recommend RESP charges, which can be calculated easily.
Step 1: Do a single point quantum chemistry calculation and save the wavefunction. For example, using Gaussian:
pincer.gjf
%nprocs=24
%mem=20GB
%chk=pincer.chk
#b3lyp/6-31g(d) geom=connectivity
tile
0 1
[ coordinates ]
After calculation, run:
$ formchk pincer.chk pincer.fchk
pincer.fchk is an ASCII file and can be used in the following calculations.
Step 2: Get Multiwfn. Do as instructed below:
$ Multiwfn pincer.fchk
$ 7 // Select "Population analysis and calculation of atomic charges"
$ 18 // Select "Restrained ElectroStatic Potential (RESP) atomic charge"
$ 1 // Select "Start standard two-stage RESP fitting calculation"
Now it will calculate electrostatic potential at 48180 points for 1736 Gaussian basis functions. Thanks to the following algorithm, the calculation can be very fast:
Tip
Zhang, J.; Lu, T. Efficient Evaluation of Electrostatic Potential with Computerized Optimized Code. Phys. Chem. Chem. Phys. 2021, 23, 20323-20328.
After calculation, you can save the charges to pincer.chg. The last column is the RESP charges. Copy them to replace the charges in pincer.psf and pincer-rigid.xyz. The finished pincer-rigid.xyz is:
pincer-rigid.xyz
98
Generated by ABCluster
O 0.97308000 4.02950000 0.02172960
O 5.22818000 4.29840000 0.55213100
O 5.45578000 2.88710000 -1.50102000
H 5.65508000 3.42840000 -0.65915200
O 1.63082000 1.39760000 -3.81621000
H 0.64178000 1.28790000 -3.63132000
O -0.85420000 1.13280000 -3.02372000
O -3.63480000 3.01800000 0.37844100
O 0.94203000 -4.12400000 -0.01164950
O 5.22756000 -4.12300000 -0.19236000
O 5.19975000 -2.75900000 1.90677000
H 5.49911000 -3.28700000 1.08741000
O 1.10372000 -1.43100000 3.83101000
H 0.13381000 -1.37300000 3.54797000
O -1.31340000 -1.31100000 2.81292000
O -3.65480000 -3.37200000 -0.81056300
N -4.55230000 1.09440000 -0.99695900
H -4.54060000 1.90820000 -0.33085600
N -4.76650000 -1.44200000 0.39144300
H -4.65210000 -2.26500000 -0.25439400
C 1.94344000 3.43050000 -0.80416400
C 3.32617000 3.54260000 -0.60306300
C 4.12217000 2.86750000 -1.60098000
C 3.56742000 2.16740000 -2.68707000
C 2.17005000 2.08920000 -2.79643000
C 1.35713000 2.72410000 -1.83511000
C -0.12610000 3.02720000 -1.80688000
C -1.12760000 1.90760000 -2.07830000
C -2.35500000 1.91710000 -1.32846000
C -2.54310000 2.90300000 -0.24390400
C -1.40410000 3.67780000 0.23983600
H -1.50880000 4.16770000 1.20107000
C -0.25120000 3.62020000 -0.44329800
C 3.98051000 4.29050000 0.46425400
C 3.18432000 5.08190000 1.47209000
H 3.87937000 5.54190000 2.17506000
H 2.48025000 4.43970000 2.00742000
H 2.58977000 5.85330000 0.97167700
C 4.46758000 1.52720000 -3.70897000
H 5.36536000 1.12230000 -3.23581000
H 4.80242000 2.26570000 -4.44793000
H 3.93826000 0.73680000 -4.24433000
C -0.45280000 4.13300000 -2.87362000
H -1.49930000 4.43910000 -2.78952000
H -0.26720000 3.72570000 -3.87041000
H 0.19468000 4.99770000 -2.70998000
C -3.38270000 0.95820000 -1.61680000
C -3.16450000 -0.17800000 -2.56830000
H -3.99600000 -0.88000000 -2.56379000
H -2.24950000 -0.71000000 -2.30253000
H -3.00750000 0.20520000 -3.58020000
C -5.75190000 0.27390000 -1.07838000
H -5.66800000 -0.41200000 -1.92466000
C -6.98160000 1.17200000 -1.28347000
H -7.04050000 1.88830000 -0.45262600
H -6.84510000 1.75430000 -2.20072000
C -8.26660000 0.33820000 -1.34828000
H -8.23510000 -0.30800000 -2.23605000
H -9.12970000 1.00130000 -1.46934000
C 1.79603000 -3.47200000 0.89376900
C 3.19591000 -3.51400000 0.81872300
C 3.86255000 -2.79400000 1.87848000
C 3.17612000 -2.10600000 2.89516000
C 1.76972000 -2.10300000 2.87705000
C 1.08107000 -2.79400000 1.86047000
C -0.37560000 -3.18400000 1.70563000
C -1.45940000 -2.12200000 1.86764000
C -2.61180000 -2.20900000 1.01188000
C -2.63740000 -3.19800000 -0.08655830
C -1.41550000 -3.90500000 -0.45472100
H -1.39180000 -4.38300000 -1.42651000
C -0.34400000 -3.78600000 0.33979400
C 3.97534000 -4.19500000 -0.20265100
C 3.31726000 -5.00200000 -1.29460000
H 4.09514000 -5.37900000 -1.95885000
H 2.60358000 -4.39700000 -1.86056000
H 2.75164000 -5.83600000 -0.86495000
C 3.94193000 -1.40900000 3.98735000
H 4.83366000 -0.92100000 3.58815000
H 4.27651000 -2.12900000 4.74422000
H 3.30842000 -0.67200000 4.48277000
C -0.73050000 -4.29800000 2.75283000
H -0.65690000 -3.87500000 3.75749000
H -0.02310000 -5.12500000 2.65752000
H -1.74630000 -4.66500000 2.58197000
C -3.69130000 -1.28100000 1.15965000
C -3.63830000 -0.14400000 2.13635000
H -4.52880000 0.47930000 2.09032000
H -2.76620000 0.47890000 1.93537000
H -3.50560000 -0.52900000 3.14983000
C -5.91880000 -0.57300000 0.21221300
H -6.00050000 0.11350000 1.05878000
C -7.19980000 -1.41500000 0.12954700
H -7.29880000 -1.99900000 1.05068000
H -7.10010000 -2.13200000 -0.69707000
C -8.42930000 -0.52700000 -0.09348310
H -9.32510000 -1.15200000 -0.17414200
H -8.57210000 0.12090000 0.78154800
par_all36_prot q epsilon (kJ/mol) sigma (AA)
-0.1977931830 0.4184 2.9400 # OG3C51
-0.5733367878 0.5021 3.1181 # OG312
-0.5300303150 0.8037 3.1449 # OG311
0.4529362989 0.1925 0.4000 # HGP1
-0.4771591324 0.8037 3.1449 # OG311
0.3642538753 0.1925 0.4000 # HGP1
-0.4651447462 0.5021 3.0291 # OG2D1
-0.5666566754 0.5021 3.0291 # OG2D1
-0.1930103667 0.4184 2.9400 # OG3C51
-0.5726160092 0.5021 3.1181 # OG312
-0.5309161679 0.8037 3.1449 # OG311
0.4526673560 0.1925 0.4000 # HGP1
-0.4711202072 0.8037 3.1449 # OG311
0.3585367639 0.1925 0.4000 # HGP1
-0.4571705592 0.5021 3.0291 # OG2D1
-0.5623143971 0.5021 3.0291 # OG2D1
-0.5765288056 0.8368 3.2963 # NG2P1
0.3467211098 0.1925 0.4000 # HGP2
-0.5967315462 0.8368 3.2963 # NG2P1
0.3529095233 0.1925 0.4000 # HGP2
0.3879440331 0.2092 3.7418 # CG2R51
-0.5788065828 0.4142 3.3141 # CG2RC0
0.3842000880 0.1674 3.7418 # CG2R64
-0.0997233426 0.3766 3.3854 # CG2R62
0.3726833554 0.1674 3.7418 # CG2R64
-0.5441667574 0.2092 3.7418 # CG2R51
0.3735821875 0.1506 3.5814 # CG3C50
0.4739123225 0.4184 3.3854 # CG2R63
-0.7130252483 0.4142 3.3141 # CG2RC0
0.6954190395 0.4184 3.3854 # CG2R63
-0.5131154947 0.3766 3.3854 # CG2R62
0.2140815465 0.1925 1.9600 # HGR62
0.1989000377 0.2092 3.7418 # CG2R51
0.7609513260 0.4602 3.5636 # CG2O1
-0.4305219061 0.3264 3.6527 # CG331
0.1157827368 0.1004 2.3876 # HGA3
0.1157827368 0.1004 2.3876 # HGA3
0.1157827368 0.1004 2.3876 # HGA3
-0.1830077140 0.3264 3.6527 # CG331
0.0728685153 0.1004 2.3876 # HGA3
0.0728685153 0.1004 2.3876 # HGA3
0.0728685153 0.1004 2.3876 # HGA3
-0.3387068233 0.3264 3.6527 # CG331
0.0997306099 0.1004 2.3876 # HGA3
0.0997306099 0.1004 2.3876 # HGA3
0.0997306099 0.1004 2.3876 # HGA3
0.6233011950 0.4602 3.5636 # CG2N2
-0.4115073756 0.3264 3.6527 # CG331
0.1347767913 0.1004 2.3876 # HGA3
0.1347767913 0.1004 2.3876 # HGA3
0.1347767913 0.1004 2.3876 # HGA3
0.2434906893 0.3766 3.3854 # CG2R62
0.0278489446 0.1883 2.3876 # HGA1
-0.1453550327 0.3766 3.3854 # CG2R62
0.0609175806 0.1464 2.3876 # HGA2
0.0609175806 0.1464 2.3876 # HGA2
-0.0163527124 0.2803 3.5543 # CG2R71
0.0239680659 0.1464 2.3876 # HGA2
0.0239680659 0.1464 2.3876 # HGA2
0.3898962115 0.2092 3.7418 # CG2R51
-0.5779944634 0.4142 3.3141 # CG2RC0
0.3856230585 0.1674 3.7418 # CG2R64
-0.1005642641 0.3766 3.3854 # CG2R62
0.3698700817 0.1674 3.7418 # CG2R64
-0.5596427812 0.2092 3.7418 # CG2R51
0.4370629855 0.1506 3.5814 # CG3C50
0.4313162857 0.4184 3.3854 # CG2R63
-0.6910763065 0.4142 3.3141 # CG2RC0
0.6777322383 0.4184 3.3854 # CG2R63
-0.4926179545 0.3766 3.3854 # CG2R62
0.2114874971 0.1925 1.9600 # HGR62
0.1640672037 0.2092 3.7418 # CG2R51
0.7567282192 0.4602 3.5636 # CG2O1
-0.4286119953 0.3264 3.6527 # CG331
0.1151360088 0.1004 2.3876 # HGA3
0.1151360088 0.1004 2.3876 # HGA3
0.1151360088 0.1004 2.3876 # HGA3
-0.1807604294 0.3264 3.6527 # CG331
0.0722453737 0.1004 2.3876 # HGA3
0.0722453737 0.1004 2.3876 # HGA3
0.0722453737 0.1004 2.3876 # HGA3
-0.3417282498 0.3264 3.6527 # CG331
0.0988146354 0.1004 2.3876 # HGA3
0.0988146354 0.1004 2.3876 # HGA3
0.0988146354 0.1004 2.3876 # HGA3
0.6378338036 0.4602 3.5636 # CG2N2
-0.4424811015 0.3264 3.6527 # CG331
0.1442920859 0.1004 2.3876 # HGA3
0.1442920859 0.1004 2.3876 # HGA3
0.1442920859 0.1004 2.3876 # HGA3
0.2524345197 0.3766 3.3854 # CG2R62
0.0249875177 0.1883 2.3876 # HGA1
-0.1457390007 0.3766 3.3854 # CG2R62
0.0617790272 0.1464 2.3876 # HGA2
0.0617790272 0.1464 2.3876 # HGA2
-0.0227826499 0.2803 3.5543 # CG2R71
0.0255840761 0.1464 2.3876 # HGA2
0.0255840761 0.1464 2.3876 # HGA2
4.4.2. Global Optimization
Now, we can do the global optimization.
Step 1: Prepare an input file named pincer-wat.inp with the following content:
pincer-wat.inp
1pincer-wat.cluster # cluster file name
2100 # population size
3100 # maximal generations
43 # scout limit
510.0 # amplitude
6pincer-wat # save optimized configuration to .xyz and .gjf
730 # number of LMs to be saved
Step 2: Prepare the cluster file named pincer-wat.cluster with the following content:
pincer-wat.cluster
12
2pincer-rigid.xyz 1
3tip4p.xyz 13
4* 20.0000
Step 3: Run the global optimization:
$ rigidmol pincer-rigid.inp > pincer-rigid.out
The global optimization is pincer-wat/1.xyz, which is shown below.
