Hi, I would like to have some clarity about this program Antechamber that can be used free of charge to convert molecular files and to apply different charge schemes and and Amber atom types. Gasteiger, Mulliken as I understand are allowed, RESP needs QM calculations, so it is clearly on the black list, but what about am1bcc?
\n\n```\n List of the File Formats
\n\n file format type abbre. index | file format type abbre. index\n --------------------------------------------------------------\n Antechamber ac 1 | Sybyl Mol2 mol2 2 \n PDB pdb 3 | Modified PDB mpdb 4 \n AMBER PREP (int) prepi 5 | AMBER PREP (car) prepc 6 \n Gaussian Z-Matrix gzmat 7 | Gaussian Cartesian gcrt 8 \n Mopac Internal mopint 9 | Mopac Cartesian mopcrt 10 \n Gaussian Output gout 11 | Mopac Output mopout 12 \n Alchemy alc 13 | CSD csd 14 \n MDL mdl 15 | Hyper hin 16 \n AMBER Restart rst 17 | Jaguar Cartesian jcrt 18 \n Jaguar Z-Matrix jzmat 19 | Jaguar Output jout 20\n Divcon Input divcrt 21 | Divcon Output divout 22\n SQM Input sqmcrt 23 | SQM Output sqmout 24\n Charmm charmm 25 | Gaussian ESP gesp 26\n Component cif ccif 27 | GAMESS dat gamess 27\n --------------------------------------------------------------\n AMBER restart file can only be read in as additional file.\n\n List of the Charge Methods \n\n charge method abbre. index | charge method abbre. index\n --------------------------------------------------------------\n RESP resp 1 | AM1-BCC bcc 2\n CM1 cm1 3 | CM2 cm2 4\n ESP (Kollman) esp 5 | Mulliken mul 6\n Gasteiger gas 7 | Read in charge rc 8\n Write out charge wc 9 | Delete Charge dc 10\n --------------------------------------------------------------\n```
", "messages": [ { "id": "550626", "postDate": "06/11/2019 20:54:21", "content": "Hi, I would like to have some clarity about this program Antechamber that can be used free of charge to convert molecular files and to apply different charge schemes and and Amber atom types. Gasteiger, Mulliken as I understand are allowed, RESP needs QM calculations, so it is clearly on the black list, but what about am1bcc?
\n\n```\n List of the File Formats
\n\n file format type abbre. index | file format type abbre. index\n --------------------------------------------------------------\n Antechamber ac 1 | Sybyl Mol2 mol2 2 \n PDB pdb 3 | Modified PDB mpdb 4 \n AMBER PREP (int) prepi 5 | AMBER PREP (car) prepc 6 \n Gaussian Z-Matrix gzmat 7 | Gaussian Cartesian gcrt 8 \n Mopac Internal mopint 9 | Mopac Cartesian mopcrt 10 \n Gaussian Output gout 11 | Mopac Output mopout 12 \n Alchemy alc 13 | CSD csd 14 \n MDL mdl 15 | Hyper hin 16 \n AMBER Restart rst 17 | Jaguar Cartesian jcrt 18 \n Jaguar Z-Matrix jzmat 19 | Jaguar Output jout 20\n Divcon Input divcrt 21 | Divcon Output divout 22\n SQM Input sqmcrt 23 | SQM Output sqmout 24\n Charmm charmm 25 | Gaussian ESP gesp 26\n Component cif ccif 27 | GAMESS dat gamess 27\n --------------------------------------------------------------\n AMBER restart file can only be read in as additional file.\n\n List of the Charge Methods \n\n charge method abbre. index | charge method abbre. index\n --------------------------------------------------------------\n RESP resp 1 | AM1-BCC bcc 2\n CM1 cm1 3 | CM2 cm2 4\n ESP (Kollman) esp 5 | Mulliken mul 6\n Gasteiger gas 7 | Read in charge rc 8\n Write out charge wc 9 | Delete Charge dc 10\n --------------------------------------------------------------\n```
", "rawMarkdown": "Hi, I would like to have some clarity about this program Antechamber that can be used free of charge to convert molecular files and to apply different charge schemes and and Amber atom types. Gasteiger, Mulliken as I understand are allowed, RESP needs QM calculations, so it is clearly on the black list, but what about am1bcc? \n\n```\n\t \t List of the File Formats \n\n\t \tfile format type abbre. index | file format type abbre. index\n\t\t--------------------------------------------------------------\n\t\tAntechamber ac 1 | Sybyl Mol2 mol2 2 \n\t\tPDB pdb 3 | Modified PDB mpdb 4 \n\t\tAMBER PREP (int) prepi 5 | AMBER PREP (car) prepc 6 \n\t\tGaussian Z-Matrix gzmat 7 | Gaussian Cartesian gcrt 8 \n\t\tMopac Internal mopint 9 | Mopac Cartesian mopcrt 10 \n\t\tGaussian Output gout 11 | Mopac Output mopout 12 \n\t\tAlchemy alc 13 | CSD csd 14 \n\t\tMDL mdl 15 | Hyper hin 16 \n\t\tAMBER Restart rst 17 | Jaguar Cartesian jcrt 18 \n\t\tJaguar Z-Matrix jzmat 19 | Jaguar Output jout 20\n\t\tDivcon Input divcrt 21 | Divcon Output divout 22\n\t\tSQM Input sqmcrt 23 | SQM Output sqmout 24\n\t\tCharmm charmm 25 | Gaussian ESP gesp 26\n\t\tComponent cif ccif 27 | GAMESS dat gamess 27\n\t\t--------------------------------------------------------------\n AMBER restart file can only be read in as additional file.\n\n\t \t List of the Charge Methods \n\n\t\tcharge method abbre. index | charge method abbre. index\n\t\t--------------------------------------------------------------\n\t\tRESP resp 1 | AM1-BCC bcc 2\n\t\tCM1 cm1 3 | CM2 cm2 4\n\t\tESP (Kollman) esp 5 | Mulliken mul 6\n\t\tGasteiger gas 7 | Read in charge rc 8\n\t\tWrite out charge wc 9 | Delete Charge dc 10\n\t\t--------------------------------------------------------------\n\n```", "votes": null }, { "id": "552014", "postDate": "06/13/2019 12:12:15", "content": "Please check the discussion below.\nhttps://www.kaggle.com/c/champs-scalar-coupling/discussion/94457#latest-551993
\n\nFrom this discussion,\nUsing antechamber is OK.\nUsing AM1BCC is not allowed because it uses semi-empirical QM calculation named AM1.\nI guess it is not allowed to use Mulliken charge obtained by antechamber because mulliken charge is a QM method in general sense.\nOn the other hand, Gasteiger charge may be acceptable. It is a completely empirical scheme.
", "rawMarkdown": "Please check the discussion below.\nhttps://www.kaggle.com/c/champs-scalar-coupling/discussion/94457#latest-551993\n\nFrom this discussion,\nUsing antechamber is OK.\nUsing AM1BCC is not allowed because it uses semi-empirical QM calculation named AM1.\nI guess it is not allowed to use Mulliken charge obtained by antechamber because mulliken charge is a QM method in general sense.\nOn the other hand, Gasteiger charge may be acceptable. It is a completely empirical scheme.", "votes": null } ], "comments": [ { "id": 552014, "author_name": "girugamess", "author_url": "", "post_date": "06/13/2019 12:12:15", "content": "Please check the discussion below.\nhttps://www.kaggle.com/c/champs-scalar-coupling/discussion/94457#latest-551993
\n\nFrom this discussion,\nUsing antechamber is OK.\nUsing AM1BCC is not allowed because it uses semi-empirical QM calculation named AM1.\nI guess it is not allowed to use Mulliken charge obtained by antechamber because mulliken charge is a QM method in general sense.\nOn the other hand, Gasteiger charge may be acceptable. It is a completely empirical scheme.
", "votes": null, "replies": [] } ], "raw_markdown_by_id": { "550626": "Hi, I would like to have some clarity about this program Antechamber that can be used free of charge to convert molecular files and to apply different charge schemes and and Amber atom types. Gasteiger, Mulliken as I understand are allowed, RESP needs QM calculations, so it is clearly on the black list, but what about am1bcc? \n\n```\n\t \t List of the File Formats \n\n\t \tfile format type abbre. index | file format type abbre. index\n\t\t--------------------------------------------------------------\n\t\tAntechamber ac 1 | Sybyl Mol2 mol2 2 \n\t\tPDB pdb 3 | Modified PDB mpdb 4 \n\t\tAMBER PREP (int) prepi 5 | AMBER PREP (car) prepc 6 \n\t\tGaussian Z-Matrix gzmat 7 | Gaussian Cartesian gcrt 8 \n\t\tMopac Internal mopint 9 | Mopac Cartesian mopcrt 10 \n\t\tGaussian Output gout 11 | Mopac Output mopout 12 \n\t\tAlchemy alc 13 | CSD csd 14 \n\t\tMDL mdl 15 | Hyper hin 16 \n\t\tAMBER Restart rst 17 | Jaguar Cartesian jcrt 18 \n\t\tJaguar Z-Matrix jzmat 19 | Jaguar Output jout 20\n\t\tDivcon Input divcrt 21 | Divcon Output divout 22\n\t\tSQM Input sqmcrt 23 | SQM Output sqmout 24\n\t\tCharmm charmm 25 | Gaussian ESP gesp 26\n\t\tComponent cif ccif 27 | GAMESS dat gamess 27\n\t\t--------------------------------------------------------------\n AMBER restart file can only be read in as additional file.\n\n\t \t List of the Charge Methods \n\n\t\tcharge method abbre. index | charge method abbre. index\n\t\t--------------------------------------------------------------\n\t\tRESP resp 1 | AM1-BCC bcc 2\n\t\tCM1 cm1 3 | CM2 cm2 4\n\t\tESP (Kollman) esp 5 | Mulliken mul 6\n\t\tGasteiger gas 7 | Read in charge rc 8\n\t\tWrite out charge wc 9 | Delete Charge dc 10\n\t\t--------------------------------------------------------------\n\n```", "552014": "Please check the discussion below.\nhttps://www.kaggle.com/c/champs-scalar-coupling/discussion/94457#latest-551993\n\nFrom this discussion,\nUsing antechamber is OK.\nUsing AM1BCC is not allowed because it uses semi-empirical QM calculation named AM1.\nI guess it is not allowed to use Mulliken charge obtained by antechamber because mulliken charge is a QM method in general sense.\nOn the other hand, Gasteiger charge may be acceptable. It is a completely empirical scheme." }, "source": "meta" }