;Ivan Gladich, Prague 26/02/2011 ; Topology file for SWM4-NDP obtained from ; ; G. Lamoureux, A. D. MacKerell, Jr., B. Roux et. al. ; A polarizable model of water for molecular dynamics simulations of biomoleculesbased on classical Drude oscillators ; Chem. Phys. Lett.,418,245-249, 2005 ; [ defaults ] ;nbfunc (1=LJ,2=Buck) 1 2 [ atomtypes ] ;name mass charge ptype sigma epsilon WO 15.99940 0.0 A 0.318395 0.88257296 WH 1.00800 0.0 A 0.0 0.0 WS 0.0 0.0 S 0.0 0.0 WD 0.0 0.0 D 0.0 0.0 [ moleculetype ] ; molname nrexcl SW 2 [ atoms ] ; id at type res nr residu name at name cg nr charge 1 WO 1 SM2 OW1 1 1.71636 2 WH 1 SM2 HW2 1 0.55733 3 WH 1 SM2 HW3 1 0.55733 4 WD 1 SM2 DW 1 -1.11466 5 WS 1 SM2 SW 1 -1.71636 [ polarization ] ; See notes above. alpha (nm^3) ;The drude particle is attached to the oxygen atom!!!!! 1 5 1 0.00097822 [ settles ] ; dHH = 0.15139 gives HOH agle equal to 104.52 degree ; i funct dOH dHH 1 1 0.09572 0.15139 ;[ constraints ] ; i funct doh dhh ;1 2 1 0.09572 ;1 3 1 0.09572 ;3 2 1 0.15139 [ virtual_sites3 ] ; The position of the dummies is computed as follows: ; ; O ; ; D ; ; H H ; "a" and "b" are wieight ;the dummy 4 is in the plane of atom 1 2 3. ;Function 2 means that rd= rO+b(rOH1+arH1H2)/|rOH1+arH1H2|(see manual) ;so a=1/2 and b the distance from the oxygen atom ; Dummy from funct a b 4 1 2 3 2 0.5 0.024034 [ exclusions ] ; iatom excluded from interaction with i 1 2 3 4 5 2 1 3 4 5 3 1 2 4 5 4 1 2 3 5 5 1 2 3 4 [ system ] Ice TIP5P-Ew T300 [ molecules ] SW 1792