F. Creation of Topology & Parameter File for
Polarizable Molecular Block Model
Describes the procedure for creating a topology & parameter file for polarizable molecular block model.
Here, topology & parameter files wth damping types S3 and G are created using trinucleotides (sGAC) as an example.
1. Concatenation of atomic charge and polarizability parameters
A trinucleotide (sGAC) is composed of seven molecular blocks as shown in Figure F1. The block molecules are MTO (methanol), DPB (DNA sugar phosphate backbone), HTF (3-hydroxytetrahydrofuran), A (adenine), G (guanine), C (cytosine), and T (thymine). The optimized atomic charges and polarizabilities of cytosine block have been determinded in 'C ESP Fitting' (fin_chg_C_red1.dat) and 'D POP Fitting' (fin_plz_s03111_01_C.dat) pages, respectively. Here we assume that the parameters for all molecular blocks have already been determined and stored in each file.
'cat_chg.cm' concatenetes optimized atomic charge files for trinucleotides (sGAC and sGTC). The concateneted atomic charges are stored in 'all_chg_GAC_red.dat' and 'all_chg_GTC_red.dat'.
Download
'cat_plz.cm' concatenetes optimized atomic polarizability files for trinucleotides (GAC and GTC). The concateneted atomic polarizabilites are stored in 'all_plz_GAC_red_s03111_one.dat' and 'all_plz_GTC_red_s03111_one.dat'.
Download
'all_chg_GAC_red.dat' file contains atomic charge data for the concatenated molecular blocks. GAC data are shown below. The atomic charges are listed in 9th column. Data for GTC can also be downloaded.
Download GAC GTC
'all_plz_GAC_red_s03111_one.dat' file contains atomic polarizability data for the concatenated molecular blocks. GAC data are shown below. The atomic polarizabilities are listed in 5th column. Data for GTC can also be downloaded.
Download GAC GTC
- Concatenation of atomic charge and polarizability parameters
- Creation of trinucleotide template file and completion of topology & parameter file for S3 type
- Creation of trinucleotide template file and completion of topology & parameter file for G type
1. Concatenation of atomic charge and polarizability parameters
A trinucleotide (sGAC) is composed of seven molecular blocks as shown in Figure F1. The block molecules are MTO (methanol), DPB (DNA sugar phosphate backbone), HTF (3-hydroxytetrahydrofuran), A (adenine), G (guanine), C (cytosine), and T (thymine). The optimized atomic charges and polarizabilities of cytosine block have been determinded in 'C ESP Fitting' (fin_chg_C_red1.dat) and 'D POP Fitting' (fin_plz_s03111_01_C.dat) pages, respectively. Here we assume that the parameters for all molecular blocks have already been determined and stored in each file.
Figure F1. Seven molecular blocks of trinucleotide and seven block molecules that make up DNA.
The asterisk marks the capped hydrogen atoms.
'cat_chg.cm' concatenetes optimized atomic charge files for trinucleotides (sGAC and sGTC). The concateneted atomic charges are stored in 'all_chg_GAC_red.dat' and 'all_chg_GTC_red.dat'.
Download
'cat_plz.cm' concatenetes optimized atomic polarizability files for trinucleotides (GAC and GTC). The concateneted atomic polarizabilites are stored in 'all_plz_GAC_red_s03111_one.dat' and 'all_plz_GTC_red_s03111_one.dat'.
Download
'all_chg_GAC_red.dat' file contains atomic charge data for the concatenated molecular blocks. GAC data are shown below. The atomic charges are listed in 9th column. Data for GTC can also be downloaded.
Download GAC GTC
'all_plz_GAC_red_s03111_one.dat' file contains atomic polarizability data for the concatenated molecular blocks. GAC data are shown below. The atomic polarizabilities are listed in 5th column. Data for GTC can also be downloaded.
Download GAC GTC
2. Creation of trinucleotide template file and completion of topology & parameter file for S3 type
Download
'top_GACst_temp_s03111.inp' and 'top_GTCst_temp_s03111.inp' are the template TopPar files. The format of each line is shown in parentheses. This template file data must be created manually and carefully. The parameters of LJ potential (emin and rmin) were taken basically from the AMBER force field (parm94). Since the new polarization terms were introduced, these were partially adjusted, referring to the QM (wB97XD/aug-cc-pVTZ) calculations for base-base stacking and base-pair hydrogen bonding interaction energies. The atomic charges and atomic polarizabilities are replaced by the optimized concatinate values (all_chg_GAC_red.dat and all_plz_GAC_red_s03111_one.dat).
Download GAC GTC
'num_blc_GAC.dat' is a file for changing the order of atoms. Change the order of atoms in 'all_chg_GAC_red.dat' and 'all_plz_GAC_red_s03111_one.dat' to the order of atoms in Gaussian 09 input file 'wB97XDaD_GAC.gjf'.
Download GAC GTC
'maketopBlc_cp.f' is a FORTRAN program for changing the order of atoms.
Download
'top_GACst_red_s03111_one.inp' is the output file of the 'maketopBlc_cp.cm' command. The optimized charges and polarizabilities have been replaced in the correct order.
Download GAC GTC
'top_r13_Na+c.inp' is a topology & parameter file of sodium ion. The polarizability of sodium ion was taken from experimental value (0.998 a.u.).
Download
'cat_top.cm' is the csh command to concatenate the GAC and GTC TopPar files. Here, the TopPar file for sodium ion is also concatenated.
Download
'top_r13_smallGACsGTCs_wB_aT_cT_s03111_one.inp' is the concatinated TopPar file for GAC, GTC, and sodium ion. This file is used in 'idffpmb_mi.cm' of 'IDFF PMB' page.
Download
'maketopBlc_cp.cm' is the csh command to create TopPar files for GAC and GTC.
1) 'all_chg_GAC_red.dat' is the input charge file. (fort.1)
2) 'all_plz_GAC_red_s03111_one.dat' is the input polarizability file. (fort.2)
3) 'top_GACst_temp_s03111_one.inp' is the template file for GAC. (fort.3)
4) 'num_blc_GAC.dat' is the file to change the order of atoms in GAC. (fort.4)
5) 'top_GACst_red_s03111_one.inp' is the output TopPar file for GAC. (fort.10)
2) 'all_plz_GAC_red_s03111_one.dat' is the input polarizability file. (fort.2)
3) 'top_GACst_temp_s03111_one.inp' is the template file for GAC. (fort.3)
4) 'num_blc_GAC.dat' is the file to change the order of atoms in GAC. (fort.4)
5) 'top_GACst_red_s03111_one.inp' is the output TopPar file for GAC. (fort.10)
Download
'top_GACst_temp_s03111.inp' and 'top_GTCst_temp_s03111.inp' are the template TopPar files. The format of each line is shown in parentheses. This template file data must be created manually and carefully. The parameters of LJ potential (emin and rmin) were taken basically from the AMBER force field (parm94). Since the new polarization terms were introduced, these were partially adjusted, referring to the QM (wB97XD/aug-cc-pVTZ) calculations for base-base stacking and base-pair hydrogen bonding interaction energies. The atomic charges and atomic polarizabilities are replaced by the optimized concatinate values (all_chg_GAC_red.dat and all_plz_GAC_red_s03111_one.dat).
1) The first line defines the residue name, total charge, dumping type (13: simple scaling), and polarizability scaling factor (1.0).(A4,f10.5,2i4,f10.5)
2) The second line ('94 0 0 94') is the number of atoms (94) .(free format)
3) The next 94 lines define the atomic species (1st column), charge (2nd column), polarizability (3rd column), and vdw rmin (7th column),
vdw emin (8th column), and molecular block number (9th column).(a2,7f10.5,i3)
The values of 2nd column are replace by the optimized atomic charges.
The values of 3rd column are replace by the optimized polarizabilities.
Atoms in the same block have the same number in the 9th column. Columns 4-6 are currently unused (0.0).
4) The next two lines define the title (20a4) and five scale factor (free format).
(charge-dipole scale factor (1.0) and dipole-dipole scale factor (1.0) for 1-5 and more (1-5+) interactions, 1-4 electrostaic (-0.5), 1-4 vdw (-0.5), and
dumping factor a. If '1-4 electrostaic' is negative, the factor is 1/1.2. If '1-4 vdw' is negative, the factor is 1/2.
'dumping factor a' is used for dumping type E1, E2, L, and G.)
5) The next two lines define the title (20a4) and two scale factors of charge-dipole and dipole-dipole for 1-2 interaction. (free format)
For dumping type S3, '1.0 0.3' is specified.
6) The next 94 lines define bond (i-j) (200i4). Define atom number i and counterpart atom number j.
To avoid double counting, j is greater than i (i<j).
7) The next two lines define the title (20a4) and two scale factors of charge-dipole (1.0) and dipole-dipole (1.0) for 1-3 interaction. (free format)
8) The next two lines define the title (20a4) and two scale factors of charge-dipole (1.0) and dipole-dipole (1.0) for 1-4 interaction. (free format)
9) The last line is blank.
2) The second line ('94 0 0 94') is the number of atoms (94) .(free format)
3) The next 94 lines define the atomic species (1st column), charge (2nd column), polarizability (3rd column), and vdw rmin (7th column),
vdw emin (8th column), and molecular block number (9th column).(a2,7f10.5,i3)
The values of 2nd column are replace by the optimized atomic charges.
The values of 3rd column are replace by the optimized polarizabilities.
Atoms in the same block have the same number in the 9th column. Columns 4-6 are currently unused (0.0).
4) The next two lines define the title (20a4) and five scale factor (free format).
(charge-dipole scale factor (1.0) and dipole-dipole scale factor (1.0) for 1-5 and more (1-5+) interactions, 1-4 electrostaic (-0.5), 1-4 vdw (-0.5), and
dumping factor a. If '1-4 electrostaic' is negative, the factor is 1/1.2. If '1-4 vdw' is negative, the factor is 1/2.
'dumping factor a' is used for dumping type E1, E2, L, and G.)
5) The next two lines define the title (20a4) and two scale factors of charge-dipole and dipole-dipole for 1-2 interaction. (free format)
For dumping type S3, '1.0 0.3' is specified.
6) The next 94 lines define bond (i-j) (200i4). Define atom number i and counterpart atom number j.
To avoid double counting, j is greater than i (i<j).
7) The next two lines define the title (20a4) and two scale factors of charge-dipole (1.0) and dipole-dipole (1.0) for 1-3 interaction. (free format)
8) The next two lines define the title (20a4) and two scale factors of charge-dipole (1.0) and dipole-dipole (1.0) for 1-4 interaction. (free format)
9) The last line is blank.
Download GAC GTC
'num_blc_GAC.dat' is a file for changing the order of atoms. Change the order of atoms in 'all_chg_GAC_red.dat' and 'all_plz_GAC_red_s03111_one.dat' to the order of atoms in Gaussian 09 input file 'wB97XDaD_GAC.gjf'.
Download GAC GTC
'maketopBlc_cp.f' is a FORTRAN program for changing the order of atoms.
Download
'top_GACst_red_s03111_one.inp' is the output file of the 'maketopBlc_cp.cm' command. The optimized charges and polarizabilities have been replaced in the correct order.
Download GAC GTC
'top_r13_Na+c.inp' is a topology & parameter file of sodium ion. The polarizability of sodium ion was taken from experimental value (0.998 a.u.).
Download
'cat_top.cm' is the csh command to concatenate the GAC and GTC TopPar files. Here, the TopPar file for sodium ion is also concatenated.
Download
'top_r13_smallGACsGTCs_wB_aT_cT_s03111_one.inp' is the concatinated TopPar file for GAC, GTC, and sodium ion. This file is used in 'idffpmb_mi.cm' of 'IDFF PMB' page.
Download
3. Creation of trinucleotide template file and completion of topology & parameter file for G type
'cat_plz_g.cm' concatenetes optimized atomic polarizability files for trinucleotides (GAC and GTC). The concateneted atomic polarizabilites are stored in 'all_plz_GAC_red_g0926_one.dat' and 'all_plz_GTC_red_g0926_one.dat'.
Download
'all_plz_GAC_red_g0926_one.dat' file contains atomic polarizability data for the concatenated molecular blocks. GAC data are shown below. The atomic polarizabilities are listed in 5th column. Data for GTC can also be downloaded.
Download GAC GTC
'maketopBlc_cp_g.cm' is the csh command to create TopPar files for GAC and GTC.
Download
'top_GACst_temp_g0926.inp' and 'top_GTCst_temp_g0926.inp' are the template TopPar files. The format of each line is shown in parentheses. This template file data must be created manually and carefully. The parameters of LJ potential (emin and rmin) were taken basically from the AMBER force field (parm94). Since the new polarization terms were introduced, these were partially adjusted, referring to the QM (wB97XD/aug-cc-pVTZ) calculations for base-base stacking and base-pair hydrogen bonding interaction energies.
Download GAC GTC
'top_GACst_red_g0926_one.inp' is the output file of the 'maketopBlc_cp.cm' command. The optimized charges and polarizabilities have been replaced in the correct order.
Download GAC GTC
'cat_top_g.cm' is the csh command to concatenate the GAC and GTC TopPar files. Here, the TopPar file for sodium ion is also concatenated.
Download
'top_r163_smallGACsGTCs_wB_aT_cT_g0926_one.inp' is the concatinated TopPar file for GAC, GTC, and sodium ion. This file is used in 'idffpmb_mi.cm' of 'IDFF PMB' page.
Download
'cat_plz_g.cm' concatenetes optimized atomic polarizability files for trinucleotides (GAC and GTC). The concateneted atomic polarizabilites are stored in 'all_plz_GAC_red_g0926_one.dat' and 'all_plz_GTC_red_g0926_one.dat'.
Download
'all_plz_GAC_red_g0926_one.dat' file contains atomic polarizability data for the concatenated molecular blocks. GAC data are shown below. The atomic polarizabilities are listed in 5th column. Data for GTC can also be downloaded.
Download GAC GTC
'maketopBlc_cp_g.cm' is the csh command to create TopPar files for GAC and GTC.
1) 'all_chg_GAC_red.dat' is the input charge file. (fort.1)
2) 'all_plz_GAC_red_g0926_one.dat' is the input polarizability file. (fort.2)
3) 'top_GACst_temp_g0926_one.inp' is the template file for GAC. (fort.3)
4) 'num_blc_GAC.dat' is the file to change the order of atoms in GAC. (fort.4)
5) 'top_GACst_red_g0926_one.inp' is the output TopPar file for GAC. (fort.10)
2) 'all_plz_GAC_red_g0926_one.dat' is the input polarizability file. (fort.2)
3) 'top_GACst_temp_g0926_one.inp' is the template file for GAC. (fort.3)
4) 'num_blc_GAC.dat' is the file to change the order of atoms in GAC. (fort.4)
5) 'top_GACst_red_g0926_one.inp' is the output TopPar file for GAC. (fort.10)
Download
'top_GACst_temp_g0926.inp' and 'top_GTCst_temp_g0926.inp' are the template TopPar files. The format of each line is shown in parentheses. This template file data must be created manually and carefully. The parameters of LJ potential (emin and rmin) were taken basically from the AMBER force field (parm94). Since the new polarization terms were introduced, these were partially adjusted, referring to the QM (wB97XD/aug-cc-pVTZ) calculations for base-base stacking and base-pair hydrogen bonding interaction energies.
1) The first line defines the residue name, total charge, dumping type (163: G type), and polarizability scaling factor (1.0).(A4,f10.5,2i4,f10.5)
2) The second line ('94 0 0 94') is the number of atoms (94) .(free format)
3) The next 94 lines define the atomic species (1st column), charge (2nd column), polarizability (3rd column), and vdw rmin (7th column),
vdw emin (8th column), and molecular block number (9th column).(a2,7f10.5,i3)
The values of 2nd column are replace by the optimized atomic charges.
The values of 3rd column are replace by the optimized polarizabilities.
Atoms in the same block have the same number in the 9th column. Columns 4-6 are currently unused (0.0).
4) The next two lines define the title (20a4) and five scale factor (free format).
(charge-dipole scale factor (1.0) and dipole-dipole scale factor (1.0) for 1-5 and more (1-5+) interactions, 1-4 electrostaic (-0.5),
1-4 vdw (-0.5), and dumping factor a. If '1-4 electrostaic' is negative, the factor is 1/1.2. If '1-4 vdw' is negative, the factor is 1/2.)
'dumping factor a' is used for dumping type E1, E2, L, and G (0.926).
5) The next two lines define the title (20a4) and two scale factors of charge-dipole and dipole-dipole for 1-2 interaction. (free format)
For dumping type G, '1.0 1.0' is specified.
6) The next 94 lines define bond (i-j) (200i4). Define atom number i and counterpart atom number j.
To avoid double counting, j is greater than i (i<j).
7) The next two lines define the title (20a4) and two scale factors of charge-dipole (1.0) and dipole-dipole (1.0) for 1-3 interaction.
(free format)
8) The next two lines define the title (20a4) and two scale factors of charge-dipole (1.0) and dipole-dipole (1.0) for 1-4 interaction.
(free format)
9) The last line is blank.
2) The second line ('94 0 0 94') is the number of atoms (94) .(free format)
3) The next 94 lines define the atomic species (1st column), charge (2nd column), polarizability (3rd column), and vdw rmin (7th column),
vdw emin (8th column), and molecular block number (9th column).(a2,7f10.5,i3)
The values of 2nd column are replace by the optimized atomic charges.
The values of 3rd column are replace by the optimized polarizabilities.
Atoms in the same block have the same number in the 9th column. Columns 4-6 are currently unused (0.0).
4) The next two lines define the title (20a4) and five scale factor (free format).
(charge-dipole scale factor (1.0) and dipole-dipole scale factor (1.0) for 1-5 and more (1-5+) interactions, 1-4 electrostaic (-0.5),
1-4 vdw (-0.5), and dumping factor a. If '1-4 electrostaic' is negative, the factor is 1/1.2. If '1-4 vdw' is negative, the factor is 1/2.)
'dumping factor a' is used for dumping type E1, E2, L, and G (0.926).
5) The next two lines define the title (20a4) and two scale factors of charge-dipole and dipole-dipole for 1-2 interaction. (free format)
For dumping type G, '1.0 1.0' is specified.
6) The next 94 lines define bond (i-j) (200i4). Define atom number i and counterpart atom number j.
To avoid double counting, j is greater than i (i<j).
7) The next two lines define the title (20a4) and two scale factors of charge-dipole (1.0) and dipole-dipole (1.0) for 1-3 interaction.
(free format)
8) The next two lines define the title (20a4) and two scale factors of charge-dipole (1.0) and dipole-dipole (1.0) for 1-4 interaction.
(free format)
9) The last line is blank.
Download GAC GTC
'top_GACst_red_g0926_one.inp' is the output file of the 'maketopBlc_cp.cm' command. The optimized charges and polarizabilities have been replaced in the correct order.
Download GAC GTC
'cat_top_g.cm' is the csh command to concatenate the GAC and GTC TopPar files. Here, the TopPar file for sodium ion is also concatenated.
Download
'top_r163_smallGACsGTCs_wB_aT_cT_g0926_one.inp' is the concatinated TopPar file for GAC, GTC, and sodium ion. This file is used in 'idffpmb_mi.cm' of 'IDFF PMB' page.
Download