Skip to content

Latest commit

 

History

History
255 lines (201 loc) · 12.5 KB

References.md

File metadata and controls

255 lines (201 loc) · 12.5 KB

aa.amber.ff03r1 Amber ff03r1 protein forcefield

Duan et al. (2003), J. Comp. Chem. 24, 1999-2012
Parameter sets obtained from AmberTools v17

aa.amber.ff14SB Amber ff14SB protein parameters

Maier et al. (2015) J. Chem. Theory Comput., 11 (8), pp 3696-3713
Parameter sets obtained from AmberTools v17

aa.amber.ff15fb Amber ff15fb protein parameters

Wang et al. (2017) J. Phys. Chem.
Parameter sets obtained from AmberTools v17

aa.amber.ff15ipq Amber ff15ipq protein parameters

Debiec et al. (2016) J. Chem. Theory Comput., 12, 3926-3947
Parameter sets obtained from AmberTools v17

aa.amber.ff94 Amber ff94 protein forcefield

Cornell et al. (1995), JACS 117, 5179-5197
Parameter sets obtained from AmberTools v17

aa.amber.ff96 Amber ff96 protein forcefield

Kollman (1996), Acc. Chem. Res. 29, 461-469
Parameter sets obtained from AmberTools v17

aa.amber.ff99 Amber ff99 protein forcefield

Wang et al. (2000), J. Comp. Chem. 21, 1049-1074
Parameter sets obtained from AmberTools v17

aa.amber.ff99SB-ILDN Amber ff99SB-ILDN protein forcefield

Lindorff-Larsen et al. (2010),  Proteins 78:1950-1958
Wang et al. (2000), J. Comp. Chem. 21, 1049-1074
Hornak et al. (2006), Proteins: Structure, Function and Genetics, 3:712-725.
Parameter sets obtained from AmberTools v17

aa.amber.ff99SB-disp Amber ff99SB-ILDN protein forcefield with additional vdw and torsion modifications. For use with water.tip4pd-1.6 model

Robustelli et al. (2018) PNAS, 115 (21) E4758-E4766
Lindorff-Larsen et al. (2010),  Proteins 78:1950-1958

aa.amber.ff99SB Amber ff99SB protein forcefield

Wang et al. (2000), J. Comp. Chem. 21, 1049-1074
Hornak et al. (2006), Proteins: Structure, Function and Genetics, 3:712-725.
Parameter sets obtained from AmberTools v17

aa.amber.ff99SBnmr Amber ff99SBnmr protein forcefield

D.W. Li and R. Bruschweiler, (2010) Angew. Chem. Int. Eng. Ed. 49:6778Wang et al. (2000), J. Comp. Chem. 21, 1049-1074
Hornak et al. (2006), Proteins: Structure, Function and Genetics, 3:712-725
Parameter sets obtained from AmberTools v17

aa.amber.ff99SBstar-ILDN Amber ff99SB*-ILDN protein forcefield

Lindorff-Larsen et al. (2010),  Proteins 78:1950-1958
Best et al. (2009), J. Phys. Chem. B. 113:9005-9015
Wang et al. (2000), J. Comp. Chem. 21:1049-1074
Hornak et al. (2006), Proteins: Structure, Function and Genetics, 3:712-725.
Parameter sets obtained from AmberTools v17

aa.amber.ffncaa Amber protein forcefield for 147 non-canonical amino acids

Khoury et al. (2014) ACS Synthetic Biology  DOI: 10.1021/sb400168u
Khoury et al  (2013) J. Chem. Theory Comput. 9 (12) 5653-5674
URL: http://selene.princeton.edu/FFNCAA/files/ffncaa.zip

aa.amber.ffptm Amber protein parameters for 32 common post-translational modifications

Khoury et al. (2014) ACS Synthetic Biology  DOI: 10.1021/sb400168u
Khoury et al  (2013) J. Chem. Theory Comput. 9 (12) 5653-5674
URL: http://selene.princeton.edu/FFPTM/files/ffptm.zip

aa.amber.phosaa10 Amber phosphorylated amino acids

Homeyer et al. (2006) J. Mol. Model. 12:281-289
Steinbrecher et al. (2012) J. Chem. Theo. Comput. 8:4405-4412
Parameter sets obtained from AmberTools v17

aa.charmm.c22 Charmm22 protein forcefield

MacKerell et al. (2004), J. Comp. Chem. 25, 1400-1415
MacKerell et al. (1998), J. Phys. Chem. B. 102, 3586-3616
URL: http://mackerell.umaryland.edu/download.php?filename=CHARMM_ff_params_files/toppar_c36_jul17.tgz

aa.charmm.c22der Charmm22 protein forcefield with modified DER side chain charges

Jensen et al. (2012) Science 336, 229-233
MacKerell et al. (2004), J. Comp. Chem. 25, 1400-1415
MacKerell et al. (1998), J. Phys. Chem. B. 102, 3586-3616
URL: http://mackerell.umaryland.edu/download.php?filename=CHARMM_ff_params_files/toppar_c36_jul17.tgz

aa.charmm.c22h Charmm22 forcefield with pseudopolarization term

Sborgi et al. (2015) J. Am. Chem. Soc. 137(20), 6506-6516
Macias et al. (2005), J. Comp. Chem. 26, 1452-1463MacKerell et al. (2004), J. Comp. Chem. 25, 1400-1415
MacKerell et al. (1998), J. Phys. Chem. B. 102, 3586-3616
URL: http://mackerell.umaryland.edu/download.php?filename=CHARMM_ff_params_files/toppar_c36_jul17.tgz

aa.charmm.c22nocmap Original charmm22 protein forcefield without added cmap terms

MacKerell et al. (1998), J. Phys. Chem. B. 102, 3586-3616
URL: http://mackerell.umaryland.edu/download.php?filename=CHARMM_ff_params_files/toppar_c36_jul17.tgz

aa.charmm.c22star Charmm22 protein forcefield with backbone and sidechain torsion and DER charge modifications

Piana et al. (2011), Biophys. J. 100, L47-L49
MacKerell et al. (2004), J. Comp. Chem. 25, 1400-1415
MacKerell et al. (1998), J. Phys. Chem. B. 102, 3586-3616
URL: http://mackerell.umaryland.edu/download.php?filename=CHARMM_ff_params_files/toppar_c36_jul17.tgz

aa.charmm.c36 Charmm36 protein forcefield

Best et al. (2012), J. Chem. Theory Comput. 8, 3257-3273
MacKerell et al. (2004), J. Comp. Chem. 25, 1400-1415
MacKerell et al. (1998), J. Phys. Chem. B. 102, 3586-3616
URL: http://mackerell.umaryland.edu/download.php?filename=CHARMM_ff_params_files/toppar_c36_jul17.tgz

aa.charmm.c36m Charmm36 protein forcefield (c36 with additional cmap and NBFIX modification)

Huang et al. (2017), Nature Methods 14, 71-73
Best et al. (2012), J. Chem. Theory Comput. 8, 3257-3273
MacKerell et al. (2004), J. Comp. Chem. 25, 1400-1415
MacKerell et al. (1998), J. Phys. Chem. B. 102, 3586-3616
URL: http://mackerell.umaryland.edu/download.php?filename=CHARMM_ff_params_files/toppar_c36_jul17.tgz

carb.charmm.c36 Charmm36 carbohydrate forcefield

Guvench et al. (2008) J. Comput. Chem. 29, 2543-2564
Hatcher et al. (2009) J Chem. Theory Comput. 5, 1315-1327
Guvench et al. (2009) J Chem. Theory Comput. 5, 2353-2370
Hatcher et al. (2009) J Phys. Chem. B. 113, 12466-76
Raman et al. (2010) J Phys. Chem. B, 114, 12981-12994
Guvench et al. (2011) J Chem. Theory Comput. 7(10), 3162-3180
Mallajosyula et al. (2011) J Phys. Chem. B 115(38), 11215-11229
Mallajosyula et al. (2012) J Chem. Theory Comput. 8(2), 759-776
URL: http://mackerell.umaryland.edu/download.php?filename=CHARMM_ff_params_files/toppar_c36_jul17.tgz

ethers.charmm.c35 Charmm35 ether forcefield

Vorobyov et al. (2007) J Chem. Theory Comput. 3, 1120-1133Lee et al. (2008) Biophys. J. 95, 1590-1599
URL: http://mackerell.umaryland.edu/download.php?filename=CHARMM_ff_params_files/toppar_c36_jul17.tgz

ions.amber1234lm_anton.spce Amber mon- di- tri- and tetra- valent ion parameters for use with spce. Stable on Anton

Li et al. (2015) J. Chem. Theory Comput., 11 (4), pp 1645-1657
12-6 monovalent ions and 12-6 iod divalent ions for spce
Parameter sets obtained from AmberTools v17

ions.amber1234lm_anton.tip3p Amber mon- di- tri- and tetra- valent ion parameters for use with tip3p. Stable on Anton

Li et al. (2015) J. Chem. Theory Comput., 11 (4), pp 1645-1657
12-6 monovalent ions and 12-6 iod divalent ions for tip3p
Parameter sets obtained from AmberTools v17

ions.amber1234lm_anton.tip4pew Amber mon- di- tri- and tetra- valent ion parameters for use with tip4pew. Stable on Anton

Li et al. (2015) J. Chem. Theory Comput., 11 (4), pp 1645-1657
12-6 monovalent ions and 12-6 iod divalent ions for tip4pew
Parameter sets obtained from AmberTools v17

ions.amber1ff99.tip3p Original Amber ion parameters contained in the ff99 forcefield

Aqvist (1990) J. Phys. Chem., 94 (21), 8021-8024
Parameter sets obtained from AmberTools v17

ions.amber1jc.spce Amber monovalent ion parameters for use with spce

Joung et al. (2008) J Phys Chem B. 112(30):9020-9041
Parameter sets obtained from AmberTools v17

ions.amber1jc.tip3p Amber monovalent ion parameters for use with tip3p

Joung et al. (2008) J Phys Chem B. 112(30):9020-9041
Parameter sets obtained from AmberTools v17

ions.amber1jc.tip4pew Amber monovalent ion parameters for use with tip4pew

Joung et al. (2008) J Phys Chem B. 112(30):9020-9041
Parameter sets obtained from AmberTools v17

ions.amber1lm_iod.all Amber monovalent ion parameters

Li et al. (2015) J. Chem. Theory Comput., 11 (4), pp 1645-1657
Parameter sets obtained from AmberTools v17

ions.charmm36 Ion parameters used with charmm36 forcefields. Includes NBFIX terms

Won et al. (2012) J. Phys. Chem A. 116, 11763-11767
Beglov et al. (1994) J. Chem. Phys 100, 9050-9063
URL: http://mackerell.umaryland.edu/download.php?filename=CHARMM_ff_params_files/toppar_c36_jul17.tgz

lipid.amber.lipid14 Amber Lipid14 parameters

Dickson et al. (2014) J. Chem. Theory Comput. 10(2) 865-879
Parameter sets obtained from AmberTools v17

lipid.amber.lipid17 Amber Lipid17 parameters

Gould et al. (2018) in prep as 'Lipid17: A Comprehensive AMBER Force Field for the Simulation of Zwitterionic and Anionic Lipids'
Parameter sets obtained from AmberTools v17

lipid.charmm.c36 Charmm36 lipid forcefield

Lim et al. (2012), J. Phys. Chem. B, 116 203-210
Klauda et al. (2012), J. Phys. Chem. B, 116  9424-9431
Klauda et al. (2010), J. Phys. Chem. B, 114, 7830-7843
URL: from http://mackerell.umaryland.edu/download.php?filename=CHARMM_ff_params_files/toppar_c36_jul17.tgz

misc.charmm.all36 Collecton of most charmm36 templates and parameters in one spot

URL: http://mackerell.umaryland.edu/download.php?filename=CHARMM_ff_params_files/toppar_c36_jul17.tgz

na.amber.OL15 Amber DNA parameters, OL15 variant

Zgarbova et al. (2015) JCTC 11: 5723
Perez et al. (2007) Biophys J. 92: 3817
Wang et al. (2000) J. Comp. Chem. 21: 1049
Parameter sets obtained from AmberTools v17

na.amber.OL3 Amber RNA parameters, OL3 variant

Zgarbova et al. (2011) JCTC 7: 2886
Perez et al. (2007) Biophys J. 92: 3817
Wang et al. (2000) J. Comp. Chem. 21: 1049
Parameter sets obtained from AmberTools v17

na.amber.ROC Amber RNA parameters, ROC variant

Aytenfisu et al. (2017) JCTC 13:900-915
Parameter sets obtained from AmberTools v17

na.amber.YIL Amber RNA parameters, YIL variant

Yildirim et al. (2011) J. Phys. Chem. B 115: 9261
Perez et al. (2007) Biophys J. 92: 3817
Wang et al. (2000) J. Comp. Chem. 21: 1049
Parameter sets obtained from AmberTools v17

na.amber.bsc1 Amber DNA parameters, bsc1 variant

Ivani et al. (2016) Nature Methods 13: 55
Perez et al. (2007) Biophys J. 92: 3817
Wang et al. (2000) J. Comp. Chem. 21: 1049
Parameter sets obtained from AmberTools v17

na.charmm.c36 Charmm36 nucleic acid forcefield

Hart et al. (2012), J Chem Theory Comput 8(1) 348-362
Denning et al. (2011), J. Comp. Chem. 32, 1929-1943
Foloppe et al. (2000), J. Comp. Chem. 21, 86-104
MacKerell et al. (2000), J. Comp. Chem. 21, 105-120
URL: http://mackerell.umaryland.edu/download.php?filename=CHARMM_ff_params_files/toppar_c36_jul17.tgz

water.spc spc 3-site water model

Berendsen et al. in Intermolecular Forces, edited by B. Pullman (Reidel, Dordrecht,1981), p. 331.

water.spc_opls spc 3-site water model with geometric combining rules for compatability with opls based forcefields

Berendsen et al. in Intermolecular Forces, edited by B. Pullman (Reidel, Dordrecht,1981), p. 331.

water.spce spce 3-site water model

Berendsen et al. (1987) J. Phys. Chem. 91, 6269.

water.tip3p-fb tip3p-fb 3-site water model

Wang et al. (2004) J. Phys. Chem. Lett. 5, 1885-1891

water.tip3p tip3p 3-site water model

Jorgensen et al. (1983) Mol. Phys. 79, 926
Parameters as tabulated in: Mahoney et al (2000) J. Chem. Phys. 112, 8910

water.tip3p_charmm tip3p 3-site water model with additional hydrogen vdw parameters. Used by charmm

Neria et al. (1996) J. Chem. Phys. 105, 1902

water.tip4p tip4p 4-site water model

Jorgensen et al. (1985) Mol. Phys. 56, 1381
Parameters as tabulated in: Mahoney et al. (2000) J. Chem. Phys. 112, 8910

water.tip4p2005 tip4p-2005 4-site water model

Vega et al. (2005) J. Chem. Phys. 123, 234505

water.tip4pd-1.6 tip4pd-1.6 water model, for use with aa.amber-disp

Robustelli et al. (2018) PNAS https://doi.org/10.1073/pnas.1800690115
Piana et al. (2015) J Phys Chem B 119:5113-5123

water.tip4pd tip4pd 4-site water model

Piana et al. (2015) J. Phys. Chem. B. 119, 5113-5123

water.tip4pew tip4pew 4-site water model

Horn et al. (2004) J. Chem. Phys. 120, 9665

water.tip5p tip5p 5-site water model

Mahoney et al. (2000) J. Chem. Phys. 112, 8910