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| Name | Modified | Size | Downloads / Week |
|---|---|---|---|
| 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 | 2 |
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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