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tbereau / auto_martini

Automatic MARTINI parametrization of small organic molecules
GNU General Public License v2.0
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how validate auto_martini itp #22

Closed georopon closed 4 years ago

georopon commented 4 years ago

Please have this output: And i like know as can validate this parameter, i'have used smiles inputs more "--fpred" command

; GENERATED WITH auto_martini.py ; ; Tristan Bereau (2014)

[moleculetype] ; molname nrexcl TDIM 2

[atoms] ; id type resnr residue atom cgnr charge smiles 1 P3 1 TDIM P01 1 0 ; CO 2 SN0 1 TDIM S01 2 0 ; c1ccccc1 3 C3 1 TDIM C01 3 0 ; CC(C)C 4 SNda 1 TDIM S02 4 0 ; Oc1ccccc1 5 SN0 1 TDIM S03 5 0 ; c1ccccc1 6 SP1 1 TDIM S04 6 0 ; Cn1cc[n+]c1 7 SQ0 1 TDIM S05 7 1 ; C[n+]1ccnc1 8 C5 1 TDIM C02 8 0 ; CC 9 C3 1 TDIM C03 9 0 ; CCC 10 C1 1 TDIM C04 10 0 ; CCCC

[bonds] ; i j funct length force.c. 1 2 1 0.24 1250 2 3 1 0.26 1250 5 6 1 0.34 1250 7 8 1 0.25 1250 8 9 1 0.32 1250 9 10 1 0.26 1250

[constraints] ; i j funct length 2 4 1 0.24 2 5 1 0.24 4 5 1 0.24 6 7 1 0.22

[angles] ; i j k funct angle force.c. 1 2 3 2 176.0 25.0 1 2 4 2 121.7 25.0 1 2 5 2 61.3 25.0 2 5 6 2 117.1 25.0 3 2 4 2 62.2 25.0 3 2 5 2 122.6 25.0 4 5 6 2 62.5 25.0 5 6 7 2 121.4 25.0 6 7 8 2 143.0 25.0 7 8 9 2 127.9 25.0 8 9 10 2 113.1 25.0

[dihedrals] ; i j k l funct angle force.c. 1 2 4 5 2 -0.5 10.0 1 2 5 4 2 179.5 10.0 1 5 2 4 2 -179.5 10.0 1 5 4 2 2 0.5 10.0 2 1 5 4 2 -0.5 10.0 2 3 4 5 2 -1.1 10.0 2 4 5 6 2 -152.8 10.0 2 4 6 5 2 29.4 10.0 2 5 4 3 2 1.2 10.0 2 5 4 6 2 152.8 10.0 2 5 6 4 2 -26.5 10.0 3 2 4 5 2 178.9 10.0 3 2 5 4 2 -1.2 10.0 3 4 2 5 2 -178.9 10.0 4 2 1 5 2 0.5 10.0 4 2 5 6 2 27.1 10.0 4 3 2 5 2 1.2 10.0 5 2 4 6 2 -33.2 10.0

tbereau commented 4 years ago

How to validate a molecule is a scientific question. It depends on the problems you want to use this for. I would recommend you to look into the literature as to how best to do this.