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Tetr 01 #107

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4cb0b87
⬆ [pre-commit.ci] pre-commit autoupdate
pre-commit-ci[bot] Jun 19, 2023
9a6e5c7
Merge pull request #105 from florianjoerg/pre-commit-ci-update-config
florianjoerg Jun 23, 2023
59cd591
⬆ [pre-commit.ci] pre-commit autoupdate
pre-commit-ci[bot] Jun 26, 2023
ab09709
Merge pull request #106 from florianjoerg/pre-commit-ci-update-config
florianjoerg Jun 27, 2023
bfe7b11
added new water files
florianjoerg Jun 27, 2023
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4 changes: 2 additions & 2 deletions .pre-commit-config.yaml
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Expand Up @@ -17,14 +17,14 @@ repos:
- id: trailing-whitespace
types: [python]
- repo: https://github.com/asottile/pyupgrade
rev: v3.4.0
rev: v3.7.0
hooks:
- id: pyupgrade
args:
- --py39-plus
- --keep-runtime-typing
- repo: https://github.com/charliermarsh/ruff-pre-commit
rev: v0.0.270
rev: v0.0.275
hooks:
- id: ruff
verbose: True
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44 changes: 20 additions & 24 deletions protex/forcefield/h2o/h2o.crd
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@@ -1,28 +1,24 @@
*~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*~ MINIMIZATION OF PACKMOL STRUCTURE
*~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
* DATE: 5/30/23 20: 8:46 CREATED BY USER: florian
* DATE: 6/27/23 15:24:34 CREATED BY USER: florian
*
22 EXT
1 1 SWM4 OH2 3.8584570147 -3.8518329640 -3.9458579610 SWM4 1 0.0000000000
2 1 SWM4 DOH2 3.9077904551 -3.8076366987 -3.9166884596 SWM4 1 0.0000000000
3 1 SWM4 H1 3.9004214972 -4.7456306929 -4.2858527285 SWM4 1 0.0000000000
4 1 SWM4 H2 3.3304234232 -3.5929924843 -3.1906004070 SWM4 1 0.0000000000
5 1 SWM4 H3 4.8142679072 -3.8012286661 -3.9360302512 SWM4 1 0.0000000000
6 1 SWM4 H4 3.6988716109 -3.5245035763 -4.8310809904 SWM4 1 0.0000000000
7 2 H3O OH2 -4.0521749261 3.9878788680 -4.2239334677 H3O 1 0.0000000000
8 2 H3O DOH2 -3.9051697108 3.8102320965 -4.1196501647 H3O 1 0.0000000000
9 2 H3O H1 -4.9497955121 4.0297687330 -3.8941542032 H3O 1 0.0000000000
10 2 H3O H2 -3.9686940105 3.3308257889 -4.9149790730 H3O 1 0.0000000000
11 2 H3O H3 -4.2770342540 4.8572895319 -4.5552870866 H3O 1 0.0000000000
12 2 H3O H4 -3.3295304416 4.2839201154 -3.6704207121 H3O 1 0.0000000000
13 3 OH OH2 3.4238068262 3.2446911657 -3.4054022876 OH 1 0.0000000000
14 3 OH DOH2 3.4619711244 3.2752725533 -3.4319014485 OH 1 0.0000000000
15 3 OH H1 2.9321461491 3.9486354645 -3.8284437088 OH 1 0.0000000000
16 3 OH H2 3.2918167711 2.4306780903 -3.8913993850 OH 1 0.0000000000
17 3 OH H3 4.3556727257 3.4633326559 -3.3980753016 OH 1 0.0000000000
18 3 OH H4 3.1113377327 3.1425180782 -2.5064275570 OH 1 0.0000000000
19 4 CLA CLA 4.1682837865 -5.2415900540 3.8235439149 CLA 1 0.0000000000
20 4 CLA DCLA 4.6002134643 -5.0154119956 4.3152742531 CLA 1 0.0000000000
21 5 SOD SOD 5.5647135695 -4.4235153719 5.1733300437 SOD 1 0.0000000000
22 5 SOD DSOD 5.7229740131 -5.1427083675 5.4447135745 SOD 1 0.0000000000
18 EXT
1 1 TOH2 OH2 1.7549251511 4.8400853520 4.7388659103 TOH2 1 0.0000000000
2 1 TOH2 DOH2 1.7780144440 4.7921848244 4.7255061636 TOH2 1 0.0000000000
3 1 TOH2 H1 1.3267829640 5.5892331202 4.3137500431 TOH2 1 0.0000000000
4 1 TOH2 H2 2.6944950646 5.0424929169 4.7774815411 TOH2 1 0.0000000000
5 1 TOH2 H3 1.5081293142 4.0192395491 4.3023391713 TOH2 1 0.0000000000
6 1 TOH2 H4 1.3784355366 4.8976213695 5.6221533987 TOH2 1 0.0000000000
7 2 TOH3 OH2 0.5449296479 0.7565878616 5.0630227267 TOH3 1 0.0000000000
8 2 TOH3 DOH2 0.6662594008 0.6549571919 4.5265547758 TOH3 1 0.0000000000
9 2 TOH3 H1 0.3638608011 0.8771667813 5.9999999971 TOH3 1 0.0000000000
10 2 TOH3 H2 1.2187856835 1.2560712715 4.5921873244 TOH3 1 0.0000000000
11 2 TOH3 H3 0.0000000034 0.3102006105 4.4080099686 TOH3 1 0.0000000000
12 2 TOH3 H4 1.0917219460 -0.0000000033 5.2950671116 TOH3 1 0.0000000000
13 3 TOH1 OH2 0.5202461282 0.7875404653 1.0399591096 TOH1 1 0.0000000000
14 3 TOH1 DOH2 0.3638608011 0.8771667813 -0.0000000028 TOH1 1 0.0000000000
15 3 TOH1 H1 0.4635825659 1.3881350837 0.2907415476 TOH1 1 0.0000000000
16 3 TOH1 H2 0.1662345469 1.3245181165 1.7552090049 TOH1 1 0.0000000000
17 3 TOH1 H3 1.4598754770 0.6027074399 0.9494878374 TOH1 1 0.0000000000
18 3 TOH1 H4 0.0498158501 0.0040807114 0.7397295670 TOH1 1 0.0000000000
82 changes: 41 additions & 41 deletions protex/forcefield/h2o/h2o.psf
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Expand Up @@ -4,46 +4,47 @@ PSF EXT CMAP CHEQ DRUDE XPLOR
*~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*~ MINIMIZATION OF PACKMOL STRUCTURE
*~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
* DATE: 5/30/23 20: 8:46 CREATED BY USER: florian

22 !NATOM
1 SWM4 1 SWM4 OH2 ODW 1.31264 15.5994 0 -0.978253 1.30000
2 SWM4 1 SWM4 DOH2 DRUD -2.42730 0.400000 0 0.00000 0.00000
3 SWM4 1 SWM4 H1 HDW 0.557330 1.00800 0 0.00000 0.00000
4 SWM4 1 SWM4 H2 HDW 0.557330 1.00800 0 0.00000 0.00000
5 SWM4 1 SWM4 H3 DUMH 0.00000 1.00800 0 0.00000 0.00000
6 SWM4 1 SWM4 H4 DUMH 0.00000 1.00800 0 0.00000 0.00000
7 H3O 1 H3O OH2 ODW 1.31263 15.5994 0 -0.978253 1.30000
8 H3O 1 H3O DOH2 DRUD -2.42730 0.400000 0 0.00000 0.00000
9 H3O 1 H3O H1 HDW 0.704890 1.00800 0 0.00000 0.00000
10 H3O 1 H3O H2 HDW 0.704890 1.00800 0 0.00000 0.00000
11 H3O 1 H3O H3 HDW 0.704890 1.00800 0 0.00000 0.00000
12 H3O 1 H3O H4 DUMH 0.00000 1.00800 0 0.00000 0.00000
13 OH 1 OH OH2 ODW 1.13410 15.5994 0 -1.00000 1.30000
14 OH 1 OH DOH2 DRUD -2.45410 0.400000 0 0.00000 0.00000
15 OH 1 OH H1 HDW 0.320000 1.00800 0 0.00000 0.00000
16 OH 1 OH H2 DUMH 0.00000 1.00800 0 0.00000 0.00000
17 OH 1 OH H3 DUMH 0.00000 1.00800 0 0.00000 0.00000
18 OH 1 OH H4 DUMH 0.00000 1.00800 0 0.00000 0.00000
19 CLA 1 CLA CLA CLAD 3.88920 35.0532 0 -3.96900 1.30000
20 CLA 1 CLA DCLA DRUD -4.88920 0.400000 0 0.00000 0.00000
21 SOD 1 SOD SOD SODD 1.97240 22.6000 0 -0.157000 1.30000
22 SOD 1 SOD DSOD DRUD -0.972400 0.400000 0 0.00000 0.00000

17 !NBOND: bonds
* DATE: 6/27/23 15:24:34 CREATED BY USER: florian

18 !NATOM
1 TOH2 1 TOH2 OH2 OPOL13 2.12540 15.5994 0 -1.42000 1.30000
2 TOH2 1 TOH2 DOH2 DPPOL -2.92440 0.400000 0 0.00000 0.00000
3 TOH2 1 TOH2 H1 HPOL 0.399500 1.00800 0 0.00000 0.00000
4 TOH2 1 TOH2 H2 HPOL 0.399500 1.00800 0 0.00000 0.00000
5 TOH2 1 TOH2 H3 DUMH 0.00000 1.00800 0 0.00000 0.00000
6 TOH2 1 TOH2 H4 DUMH 0.00000 1.00800 0 0.00000 0.00000
7 TOH3 1 TOH3 OH2 OPOL13 2.07510 15.5994 0 -1.09000 1.30000
8 TOH3 1 TOH3 DOH2 DPPOL -2.56220 0.400000 0 0.00000 0.00000
9 TOH3 1 TOH3 H1 HPOL 0.495700 1.00800 0 0.00000 0.00000
10 TOH3 1 TOH3 H2 HPOL 0.495700 1.00800 0 0.00000 0.00000
11 TOH3 1 TOH3 H3 HPOL 0.495700 1.00800 0 0.00000 0.00000
12 TOH3 1 TOH3 H4 DUMH 0.00000 1.00800 0 0.00000 0.00000
13 TOH1 1 TOH1 OH2 OPOL13 3.59500 15.5994 0 -3.95000 1.30000
14 TOH1 1 TOH1 DOH2 DPPOL -4.87750 0.400000 0 0.00000 0.00000
15 TOH1 1 TOH1 H1 HPOL 0.282500 1.00800 0 0.00000 0.00000
16 TOH1 1 TOH1 H2 DUMH 0.00000 1.00800 0 0.00000 0.00000
17 TOH1 1 TOH1 H3 DUMH 0.00000 1.00800 0 0.00000 0.00000
18 TOH1 1 TOH1 H4 DUMH 0.00000 1.00800 0 0.00000 0.00000

15 !NBOND: bonds
1 2 1 3 1 4 1 5
1 6 7 8 7 9 7 10
7 11 7 12 13 14 13 15
13 16 13 17 13 18 19 20
21 22

18 !NTHETA: angles
3 1 4 3 1 5 3 1 6
4 1 5 4 1 6 5 1 6
9 7 10 9 7 11 9 7 12
10 7 11 10 7 12 11 7 12
15 13 16 15 13 17 15 13 18
16 13 17 16 13 18 17 13 18
13 16 13 17 13 18

36 !NTHETA: angles
3 1 4 3 1 4 3 1 5
3 1 5 3 1 6 3 1 6
4 1 5 4 1 6 4 1 6
5 1 4 5 1 6 5 1 6
9 7 10 9 7 10 9 7 11
9 7 11 9 7 12 9 7 12
10 7 11 10 7 12 10 7 12
11 7 10 11 7 12 11 7 12
15 13 16 15 13 16 15 13 17
15 13 17 15 13 18 15 13 18
16 13 17 16 13 18 16 13 18
17 13 16 17 13 18 17 13 18

0 !NPHI: dihedrals

Expand All @@ -61,16 +62,15 @@ PSF EXT CMAP CHEQ DRUDE XPLOR

0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0
0 0 0 0 0 0
0 0

5 0 !NGRP NST2
3 0 !NGRP NST2
0 1 0 6 2 0 12 2 0
18 2 0 20 2 0

1 !MOLNT
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1
1 1

0 0 !NUMLP NUMLPH

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25 changes: 13 additions & 12 deletions protex/forcefield/h2o/h2o_d.str
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Expand Up @@ -17,23 +17,24 @@ AUTO ANGL DIHE DRUD
! Alpha and Thole values are picked from first match of atom type in a text file containing all currently available residues.
! If it cannot find the values -1.0 and -1.3 values are assigned to the atom type.

RESI SWM4 0.000 ! SWM4-NDP water
!TETRA-WATER by Max
RESI TOH2 0.0000
GROUP
ATOM OH2 ODW -1.11466 ALPHA -0.97825258 THOLE 1.3
ATOM H1 HDW 0.55733
ATOM H2 HDW 0.55733
ATOM H3 DUMH 0.000
ATOM H4 DUMH 0.000
ATOM OH2 OPOL13 -0.7990 TYPE DPPOL ALPHA -1.42 THOLE 1.3
ATOM H1 HPOL 0.3995
ATOM H2 HPOL 0.3995
ATOM H3 DUMH 0.0000
ATOM H4 DUMH 0.0000
BOND OH2 H1
BOND OH2 H2
BOND OH2 H3
BOND OH2 H4
!ANGLE H1 OH2 H2
!ANGLE H1 OH2 H3
!ANGLE H3 OH2 H2
!ANGLE H1 OH2 H4
!ANGLE H2 OH2 H4
!ANGLE H3 OH2 H4
ANGLE H1 OH2 H2
ANGLE H1 OH2 H3
ANGLE H3 OH2 H2
ANGLE H1 OH2 H4
ANGLE H2 OH2 H4
ANGLE H3 OH2 H4


PATCH FIRST NONE LAST NONE
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19 changes: 19 additions & 0 deletions protex/forcefield/h2o/h2o_init.crd
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@@ -0,0 +1,19 @@
* Packmol generated pdb file
* Home-Page: http://m3g.iqm.unicamp.br/packmol
*
15 EXT
1 1 TOH2 OH2 -1.2370000000 2.1500000000 1.9550000000 TOH2 1 0.0000000000
2 1 TOH2 H1 -1.7050000000 2.9630000000 1.3810000000 TOH2 1 0.0000000000
3 1 TOH2 H2 -0.1470000000 2.3010000000 1.9830000000 TOH2 1 0.0000000000
4 1 TOH2 H3 -1.4580000000 1.1950000000 1.4780000000 TOH2 1 0.0000000000
5 1 TOH2 H4 -1.6290000000 2.1480000000 2.9710000000 TOH2 1 0.0000000000
6 2 TOH3 OH2 -2.2620000000 -2.1790000000 2.2290000000 TOH3 1 0.0000000000
7 2 TOH3 H1 -2.8110000000 -1.6180000000 3.0000000000 TOH3 1 0.0000000000
8 2 TOH3 H2 -1.5620000000 -1.5050000000 1.7130000000 TOH3 1 0.0000000000
9 2 TOH3 H3 -2.9680000000 -2.5900000000 1.5070000000 TOH3 1 0.0000000000
10 2 TOH3 H4 -1.7060000000 -2.9910000000 2.6970000000 TOH3 1 0.0000000000
11 3 TOH1 OH2 -2.3900000000 -2.0160000000 -2.0540000000 TOH1 1 0.0000000000
12 3 TOH1 H1 -2.5500000000 -1.3830000000 -2.9400000000 TOH1 1 0.0000000000
13 3 TOH1 H2 -2.7460000000 -1.4890000000 -1.1560000000 TOH1 1 0.0000000000
14 3 TOH1 H3 -1.3260000000 -2.2310000000 -1.9500000000 TOH1 1 0.0000000000
15 3 TOH1 H4 -2.9400000000 -2.9490000000 -2.1690000000 TOH1 1 0.0000000000
25 changes: 13 additions & 12 deletions protex/forcefield/h2o/h3o_d.str
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Expand Up @@ -17,23 +17,24 @@ AUTO ANGL DIHE DRUD
! Alpha and Thole values are picked from first match of atom type in a text file containing all currently available residues.
! If it cannot find the values -1.0 and -1.3 values are assigned to the atom type.

RESI H3O 1.000 ! SWM4-NDP water
!TETRA-WATER by Max
RESI TOH3 1.0000
GROUP
ATOM OH2 ODW -1.11467 ALPHA -0.97825258 THOLE 1.3
ATOM H1 HDW 0.70489
ATOM H2 HDW 0.70489
ATOM H3 HDW 0.70489
ATOM H4 DUMH 0.000
ATOM OH2 OPOL13 -0.4871 TYPE DPPOL ALPHA -1.09 THOLE 1.3
ATOM H1 HPOL 0.4957
ATOM H2 HPOL 0.4957
ATOM H3 HPOL 0.4957
ATOM H4 DUMH 0.0000
BOND OH2 H1
BOND OH2 H2
BOND OH2 H3
BOND OH2 H4
!ANGLE H1 OH2 H2
!ANGLE H1 OH2 H3
!ANGLE H3 OH2 H2
!ANGLE H1 OH2 H4
!ANGLE H2 OH2 H4
!ANGLE H3 OH2 H4
ANGLE H1 OH2 H2
ANGLE H1 OH2 H3
ANGLE H3 OH2 H2
ANGLE H1 OH2 H4
ANGLE H2 OH2 H4
ANGLE H3 OH2 H4

PATCH FIRST NONE LAST NONE

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12 changes: 12 additions & 0 deletions protex/forcefield/h2o/initialize.sh
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@@ -0,0 +1,12 @@
#!/bin/bash

###change###
filename="h2o"
#############

echo "Running packmol..."
/home/andras/git/packmol/packmol < packmol.inp > packmol.out
echo "Running pdb2crd..."
/home/marta/bin/pdb2corv2 ${filename}_init.pdb > ${filename}_init.crd
echo "Running CHARMM, create psf, crd..."
charmm -i write_psf_crd.inp -o write_psf_crd.out
2 changes: 1 addition & 1 deletion protex/forcefield/h2o/na_d.str
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Expand Up @@ -16,7 +16,7 @@ AUTO ANGL DIHE DRUD

RESI SOD 1.000 ! Sodium Ion
GROUP
ATOM SOD SODD 1.000 ALPHA -0.157
ATOM SOD SODD 1.000 ALPHA -0.157
PATCHING FIRST NONE LAST NONE

END
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