Name | Modified | Size | Downloads / Week |
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Lysozyme-NAG3_DDT_MD.zip | 2019-05-08 | 1.9 MB | |
DDT_water_MD.zip | 2019-05-08 | 599.0 kB | |
README_sam19.txt | 2019-05-07 | 5.7 kB | |
sam19.ff.zip | 2019-05-07 | 55.3 kB | |
Totals: 4 Items | 2.6 MB | 0 |
------------------------------------------------------------- SAM19: A Refined Empirical Force Field to Model Protein-SAM Interactions Based on AMBER14 and GAFF ------------------------------------------------------------- Provided by: Computational Biology and Bioinformatics Lab University of Macau pratiti.bhadra@gmail.com shirleysiu@um.edu.mo http://cbbio.cis.umac.mo Tested on: GROMACS 5.0.5 ------------------------------------------------------------- CITATION: Bhadra and Siu, A Refined Empirical Force Field to Model Protein-SAM Interactions Based on AMBER14 and GAFF, 2019. (submitted) ACKNOWLEDGEMENT: The amber14sb.ff parameters are kindly provided by Kristyna Pluhackova. FUNDING: FDCT (066/2016/A) by Macau SAR; MYRG2014-00104-FST & MYRG2015-00212-FST by University of Macau ------------------------------------------------------------- Our work started from amber14sb.ff. Initially, amber14sb.ff was created based on amber99sb-idln.ff by Kristyna and others from Friedrich-Alexander University Erlangen-Nürnberg, Germany. We added the following files to the force field directory amber14sb.ff for the Self-Assembled Monolayer system (SAM). Currently, only the alkanethiol (CH3) function group is implemented; the SAM ligand (DDT) is taken as one residue with 12 carbon segments. The SAM should be built on a layer of substrate, here we implemented the gold atom (AU). (1) DDT.itp (C12 SAM ligand) (2) DDT.pdb (C12 SAM ligand) (3) AU.itp (Gold atom for the substrate) We updated following files on top of amber14sb.ff to incorporate our tuned force field parameters for protein-SAM interactions: (1) aminoacids.rtp atom types of LYS, ASP, ASN, ARG, GLU, GLN were modified ASP: CG COF; OD1 O2F; OD2 O2F LYS: NZ NF3; HZ1 HF; HZ2 HF; HZ3 HF ASN: CG CF; OD1 OF; ND2 NF; HD21 HF;HD21 HF ARG: NE NF2; HE HF; NH1 NF2; HH11 HF;HH12 HF; NH2 NF2; HH21 HF; HH22 HF GLU: CD COF; OE1 O2F; OE2 O2F; GNL: CD CF; OE1 OF; NE2 NF; HE21 HF;HE22 HF (2) ffnonbonded.itp [ atomtypes ] AU 79 196.967 0.0000 A 2.935e-01 0.163176e+00 ; added by Pratiti ; NF3 7 14.01 0.0000 A 3.25000e-01 7.11280e-01 ; added by pratiti LYS N3 IFF NF2 7 14.01 0.0000 A 3.25000e-01 7.11280e-01 ; added by pratiti ARG N2 IFF NF 7 14.01 0.0000 A 3.25000e-01 7.11280e-01 ; added by pratiti ARG N2 IFF HF 1 1.008 0.0000 A 1.95998e-01 6.56888e-02 ; added by pratiti LYS ARG H IFF COF 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 ; added by pratiti ASP GLU CO IFF O2F 8 16.00 0.0000 A 2.95992e-01 8.78640e-01 ; added by pratiti ASP GLU CO IFF CF 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 ; added by pratiti ASN GLN CO IFF OF 8 16.00 0.0000 A 2.95992e-01 8.78640e-01 ; added by pratiti ASN GLN CO IFF c3 6 12.01 0.0000 A 3.39967e-01 4.57730e-01 ; Pratiti gaff SAM hx 1 1.008 0.0000 A 1.95998e-01 6.56888e-02 ; Pratiti gaff SAM hn 1 1.008 0.0000 A 1.06908e-01 6.56888e-02 ; Pratiti gaff SAM hc 1 1.008 0.0000 A 2.64953e-01 6.56888e-02 ; Pratiti gaff SAM h1 1 1.008 0.0000 A 2.47135e-01 6.56888e-02 ; Pratiti gaff SAM ho 1 1.008 0.0000 A 0.00000e+00 0.00000e+00 ; Pratiti gaff SAM n3 7 14.01 0.0000 A 3.25000e-01 7.11280e-01 ; Pratiti gaff SAM n4 7 14.01 0.0000 A 3.25000e-01 7.11280e-01 ; Pratiti gaff SAM oh 8 16.00 0.0000 A 3.06647e-01 8.80314e-01 ; Pratiti gaff SAM s 16 32.06 0.0000 A 3.56359e-01 1.04600e+00 ; Pratiti gaff SAM o 8 16.00 0.0000 A 2.95992e-01 8.78640e-01 ; Pratiti gaff SAM c 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 ; Pratiti gaff SAM [nonbond_params] ; added by PRATITI ; i j func sigma epilson NF3 c3 1 3.32484e-01 8.55887e-01 ; *1.5 NF2 c3 1 3.32484e-01 8.55887e-01 ; *1.5 NF c3 1 3.32484e-01 8.55887e-01 ; *1.5 HF c3 1 2.23438e-01 2.60101e-01 ; *1.5 NF3 HC 1 2.94977e-01 8.64621e-01 ; *4 NF2 HC 1 2.94977e-01 8.64621e-01 ; *4 NF HC 1 2.94977e-01 8.64621e-01 ; *4 HF HC 1 1.85931e-01 2.62755e-01 ; *4 O2F c3 1 3.17980e-01 9.51265e-01 ; *1.5 c3-OX O2F HC 1 2.80472e-01 9.39305e-01 ; *4 new COF HC 1 3.02460e-01 9.22448e-01 ; *6 CO-HC COF c3 1 3.39967e-01 9.13129e-01 ; *2.25 CO-c3 OF c3 1 3.17980e-01 9.51265e-01 ; *1.5 c3-OF CF c3 1 3.39967e-01 9.13129e-01 ; *2.25 C-c3 OF HC 1 2.80472e-01 9.39305e-01 ; *4 new (3) atomtypes.atp HF 1.00800 O2F 16.00000 OF 16.00000 COF 12.01000 CF 12.01000 NF3 14.01000 NF2 14.01000 NF 14.01000 AU 196.967 Accordingly ffbonded.itp is also updated