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rsdefever/emim.gro Secret

Created June 25, 2021 14:39
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parmed->gmso layered dihedrals failure
Raw
emim.gro
GROningen MAchine for Chemical Simulation
19
1EMI C 1 -0.057 -0.089 -0.118
1EMI C1 2 -0.015 0.034 -0.078
1EMI H 3 -0.295 -0.000 0.083
1EMI H1 4 -0.012 -0.159 -0.186
1EMI H2 5 0.072 0.091 -0.104
1EMI N 6 -0.111 0.082 0.010
1EMI N1 7 -0.177 -0.115 -0.055
1EMI C2 8 -0.207 -0.009 0.022
1EMI C3 9 -0.107 0.213 0.077
1EMI H3 10 -0.107 0.292 0.003
1EMI H4 11 -0.195 0.223 0.140
1EMI H5 12 -0.017 0.219 0.139
1EMI C4 13 -0.257 -0.239 -0.067
1EMI H6 14 -0.356 -0.216 -0.029
1EMI H7 15 -0.267 -0.260 -0.174
1EMI C5 16 -0.194 -0.356 0.007
1EMI H8 17 -0.095 -0.381 -0.032
1EMI H9 18 -0.185 -0.335 0.114
1EMI H10 19 -0.258 -0.444 -0.005
0.56150 0.61230 0.87840
Raw
emim_fake.top
;
; File emim.top was generated
; By user: rdefever (239529)
; On host: maginnfe.crc.nd.edu
; At date: Tue. December 2 16:02:23 2020
;
; This is a standalone topology file
;
; Created by:
; ParmEd: create_gmx.py, VERSION 3.2.0
; Executable: create_gmx.py
; Library dir: /usr/local/gromacs/share/gromacs/top
; Command line:
; create_gmx.py
;
[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 2 yes 0.5 0.83333333
[ atomtypes ]
; name at.num mass charge ptype sigma epsilon
cc 6 12.010000 0.00000000 A 0.33996695 0.359824
cd 6 12.010000 0.00000000 A 0.33996695 0.359824
h5 1 1.008000 0.00000000 A 0.24214627 0.06276
h4 1 1.008000 0.00000000 A 0.25105526 0.06276
na 7 14.010000 0.00000000 A 0.32499985 0.71128
c3 6 12.010000 0.00000000 A 0.33996695 0.4577296
h1 1 1.008000 0.00000000 A 0.2471353 0.0656888
hc 1 1.008000 0.00000000 A 0.26495328 0.0656888
[ moleculetype ]
; Name nrexcl
EMI 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB chargeB massB
; residue 1 RES rtp RES q 1.0
1 cc 1 EMI C 1 -0.141000 12.010000 ; qtot -0.115300
2 cd 1 EMI C1 2 -0.163000 12.010000 ; qtot -0.235600
3 h5 1 EMI H 3 0.186000 1.008000 ; qtot 0.020400
4 h4 1 EMI H1 4 0.197000 1.008000 ; qtot 0.253400
5 h4 1 EMI H2 5 0.191000 1.008000 ; qtot 0.487400
6 na 1 EMI N 6 0.215000 14.010000 ; qtot 0.470300
7 na 1 EMI N1 7 0.072000 14.010000 ; qtot 0.452200
8 cc 1 EMI C2 8 -0.111000 12.010000 ; qtot 0.417600
9 c3 1 EMI C3 9 -0.310000 12.010000 ; qtot 0.412200
10 h1 1 EMI H3 10 0.146000 1.008000 ; qtot 0.509900
11 h1 1 EMI H4 11 0.146000 1.008000 ; qtot 0.601600
12 h1 1 EMI H5 12 0.146000 1.008000 ; qtot 0.700300
13 c3 1 EMI C4 13 -0.024000 12.010000 ; qtot 0.718600
14 h1 1 EMI H6 14 0.087000 1.008000 ; qtot 0.809300
15 h1 1 EMI H7 15 0.087000 1.008000 ; qtot 0.909000
16 c3 1 EMI C5 16 -0.128000 12.010000 ; qtot 0.782900
17 hc 1 EMI H8 17 0.068000 1.008000 ; qtot 0.849600
18 hc 1 EMI H9 18 0.068000 1.008000 ; qtot 0.910300
19 hc 1 EMI H10 19 0.068000 1.008000 ; qtot 1.000000
[ bonds ]
; ai aj funct c0 c1 c2 c3
1 2 1 0.13710 421747.200000
1 7 1 0.13710 367187.840000
2 6 1 0.13710 367187.840000
6 8 1 0.13710 367187.840000
6 9 1 0.14560 280076.960000
7 8 1 0.13710 367187.840000
7 13 1 0.14560 280076.960000
13 16 1 0.15350 253634.080000
1 4 1 0.10830 292963.680000
2 5 1 0.10830 292963.680000
3 8 1 0.10790 297900.800000
9 10 1 0.10930 281081.120000
9 11 1 0.10930 281081.120000
9 12 1 0.10930 281081.120000
13 14 1 0.10930 281081.120000
13 15 1 0.10930 281081.120000
16 17 1 0.10920 282252.640000
16 18 1 0.10920 282252.640000
16 19 1 0.10920 282252.640000
[ pairs ]
; ai aj funct c0 c1 c2 c3
1 9 1
1 16 1
2 13 1
6 13 1
7 9 1
8 16 1
1 3 1
1 14 1
1 15 1
2 3 1
2 10 1
2 11 1
2 12 1
3 9 1
3 13 1
4 5 1
4 6 1
4 8 1
4 13 1
7 5 1
5 8 1
5 9 1
7 17 1
7 18 1
7 19 1
8 10 1
8 11 1
8 12 1
8 14 1
8 15 1
14 17 1
14 18 1
14 19 1
15 17 1
15 18 1
15 19 1
[ angles ]
; ai aj ak funct c0 c1 c2 c3
1 2 6 1 109.4200471 610.110880
1 7 8 1 109.9000471 576.889920
1 7 13 1 125.0900538 523.502080
2 1 7 1 109.4200471 610.110880
2 6 8 1 128.0100547 534.547840
2 6 9 1 125.0900538 523.502080
6 8 7 1 109.3300469 616.303200
7 13 16 1 112.8100482 550.028640
8 6 9 1 125.0900538 523.502080
8 7 13 1 125.0900538 523.502080
1 2 5 1 129.1100552 394.885920
2 1 4 1 129.1100552 394.885920
3 8 6 1 122.1000523 416.391680
3 8 7 1 122.1000523 416.391680
4 1 7 1 119.6600514 420.240960
5 2 6 1 119.6600514 420.240960
6 9 10 1 109.4500472 417.563200
6 9 11 1 109.4500472 417.563200
6 9 12 1 109.4500472 417.563200
7 13 14 1 109.4500472 417.563200
7 13 15 1 109.4500472 417.563200
10 9 11 1 109.5500472 327.858240
10 9 12 1 109.5500472 327.858240
11 9 12 1 109.5500472 327.858240
13 16 17 1 110.0500475 388.024160
13 16 18 1 110.0500475 388.024160
13 16 19 1 110.0500475 388.024160
14 13 15 1 109.5500472 327.858240
14 13 16 1 110.0700471 387.940480
15 13 16 1 110.0700471 387.940480
17 16 18 1 108.3500467 329.950240
17 16 19 1 108.3500467 329.950240
18 16 19 1 108.3500467 329.950240
[ dihedrals ]
; ai aj ak al funct c0 c1 c2 c3 c4 c5
1 2 6 8 1 180.0000771 7.1128000 2
1 2 6 8 1 180.0000771 7.1128000 3
1 7 8 6 1 180.0000771 7.1128000 2
[ system ]
; Name
Generic title
[ molecules ]
; Compound #mols
EMI 1
Raw
failure.py
import parmed
from gmso.external import from_parmed
pmd = parmed.load_file("emim_fake.top", xyz="emim.gro")
top = from_parmed(pmd)
print(top.dihedral_types)
print(pmd.dihedrals)
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