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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      





Source: README_sam19.txt, updated 2019-05-07