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wdelano |
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#define EXTERN extern |
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#include "pcwin.h" |
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#include "pcmod.h" |
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#include "bonds_ff.h" |
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#include "angles.h" |
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#include "field.h" |
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#include "attached.h" |
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#define STILL 1 |
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#define HCT 2 |
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EXTERN struct t_solvent { |
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int type; |
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double EPSin, EPSsolv; |
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double doffset, p1,p2,p3,p4,p5; |
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double *shct,*asolv,*rsolv,*vsolv,*gpol,*rborn; |
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} solvent; |
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int find_bond(int,int); |
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void born(void); |
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void ksolv(void); |
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void message_alert(char *, char *); |
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// choices are gbsa models: Analytical Still and HCT |
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// allocate memory in get_mem |
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void ksolv() |
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{ |
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int i,j,k, jji,it,kt; |
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int ia,ib,ic,id; |
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double ri,ri2,rk,cc; |
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double r,r2,r4,rab,rbc; |
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double cosine,factor; |
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double h,ratio,term; |
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solvent.doffset = -0.09; |
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solvent.p1 = 0.073; |
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solvent.p2 = 0.921; |
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solvent.p3 = 6.211; |
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solvent.p4 = 15.236; |
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solvent.p5 = 1.254; |
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if (solvent.type == HCT) |
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{ |
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for (i=1; i <= natom; i++) |
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{ |
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solvent.asolv[i] = 0.0054; |
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solvent.shct[i] = 0.0; |
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if (atom[i].atomnum == 1) solvent.shct[i] = 0.85; |
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if (atom[i].mmx_type == 20) solvent.shct[i] = 0.85; |
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if (atom[i].atomnum == 6) solvent.shct[i] = 0.72; |
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if (atom[i].atomnum == 7) solvent.shct[i] = 0.79; |
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if (atom[i].atomnum == 8) solvent.shct[i] = 0.85; |
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if (atom[i].atomnum == 9) solvent.shct[i] = 0.88; |
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if (atom[i].atomnum == 15) solvent.shct[i] = 0.86; |
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if (atom[i].atomnum == 16) solvent.shct[i] = 0.96; |
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if (atom[i].atomnum == 26) solvent.shct[i] = 0.88; |
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} |
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} else if (solvent.type == STILL) |
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{ |
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for (i=1; i <= natom; i++) |
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{ |
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solvent.asolv[i] = 0.0049; |
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} |
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} |
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// assign standard radii |
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for (i=1; i <= natom; i++) |
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{ |
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solvent.rsolv[i] = 0.0; |
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if (atom[i].atomnum == 1) |
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{ |
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solvent.rsolv[i] = 1.25; |
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if (atom[atom[i].iat[0]].atomnum == 7) solvent.rsolv[i] = 1.15; |
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if (atom[atom[i].iat[0]].atomnum == 8) solvent.rsolv[i] = 1.05; |
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} else if (atom[i].mmx_type == 20) |
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{ |
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solvent.rsolv[i] = 0.8; |
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} else if (atom[i].atomnum == 3) |
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{ |
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solvent.rsolv[i] = 1.432; |
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} else if (atom[i].atomnum == 6) |
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{ |
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solvent.rsolv[i] = 1.90; |
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jji = 0; |
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for (j=0; j < 4; j++) |
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{ |
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if (atom[i].iat[j] != 0) |
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jji++; |
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} |
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if (jji == 3) solvent.rsolv[i] = 1.875; |
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if (jji == 2) solvent.rsolv[i] = 1.825; |
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} else if (atom[i].atomnum == 7) |
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{ |
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solvent.rsolv[i] = 1.7063; |
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jji = 0; |
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for (j=0; j < 4; j++) |
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{ |
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if (atom[i].iat[j] != 0) |
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jji++; |
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} |
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if (jji == 4) solvent.rsolv[i] = 1.625; |
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if (jji == 1) solvent.rsolv[i] = 1.60; |
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} else if (atom[i].atomnum == 8) |
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{ |
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solvent.rsolv[i] = 1.535; |
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jji = 0; |
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for (j=0; j < 4; j++) |
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{ |
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if (atom[i].iat[j] != 0) |
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jji++; |
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} |
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if (jji == 1) solvent.rsolv[i] = 1.48; |
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} else if (atom[i].atomnum == 9) |
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{ |
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solvent.rsolv[i] = 1.47; |
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} else if (atom[i].atomnum == 10) |
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{ |
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solvent.rsolv[i] = 1.39; |
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} else if (atom[i].atomnum == 11) |
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{ |
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solvent.rsolv[i] = 1.992; |
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} else if (atom[i].atomnum == 12) |
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{ |
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solvent.rsolv[i] = 1.70; |
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} else if (atom[i].atomnum == 14) |
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{ |
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solvent.rsolv[i] = 1.80; |
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} else if (atom[i].atomnum == 15) |
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{ |
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solvent.rsolv[i] = 1.87; |
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} else if (atom[i].atomnum == 16) |
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{ |
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solvent.rsolv[i] = 1.775; |
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} else if (atom[i].atomnum == 17) |
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{ |
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solvent.rsolv[i] = 1.735; |
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} else if (atom[i].atomnum == 18) |
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{ |
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solvent.rsolv[i] = 1.70; |
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} else if (atom[i].atomnum == 19) |
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{ |
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solvent.rsolv[i] = 2.123; |
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} else if (atom[i].atomnum == 20) |
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{ |
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solvent.rsolv[i] = 1.817; |
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} else if (atom[i].atomnum == 35) |
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{ |
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solvent.rsolv[i] = 1.90; |
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} else if (atom[i].atomnum == 36) |
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{ |
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solvent.rsolv[i] = 1.812; |
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} else if (atom[i].atomnum == 37) |
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{ |
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solvent.rsolv[i] = 2.26; |
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} else if (atom[i].atomnum == 53) |
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{ |
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solvent.rsolv[i] = 2.10; |
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} else if (atom[i].atomnum == 54) |
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{ |
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solvent.rsolv[i] = 1.967; |
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} else if (atom[i].atomnum == 55) |
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{ |
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solvent.rsolv[i] = 2.507; |
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} else if (atom[i].atomnum == 56) |
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{ |
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solvent.rsolv[i] = 2.188; |
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}else |
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{ |
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message_alert("Error - Atom not available for GB/SA","Error"); |
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break; |
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} |
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} |
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// atomic volumes for Still |
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if (solvent.type == STILL) |
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{ |
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for (i=1; i <= natom; i++) |
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{ |
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if (atom[i].mmx_type != 20) |
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{ |
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solvent.vsolv[i] = (4.0*PI/3.0)*solvent.rsolv[i]*solvent.rsolv[i]*solvent.rsolv[i]; |
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ri = solvent.rsolv[i]; |
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ri2 = ri*ri; |
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for (j=0; j < MAXIAT; j++) |
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{ |
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if (atom[i].iat[j] != 0 && atom[i].bo[j] != 9 && atom[atom[i].iat[j]].mmx_type != 20) |
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{ |
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k = find_bond(i,atom[i].iat[j]); |
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rk = solvent.rsolv[atom[i].iat[j]]; |
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r = 1.01 * bonds_ff.bl[k]; |
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ratio = (rk*rk - ri2 - r*r)/(2.0*ri*r); |
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h = ri*(1.0+ratio); |
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term = (PI/3.0)*h*h*(3.0*ri-h); |
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solvent.vsolv[i] -= term; |
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} |
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} |
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} |
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} |
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// 1,2 and 1,3 polarization |
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cc = 4.80298*4.80298*14.39418; |
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for (i=1; i <= natom; i++) |
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{ |
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if (atom[i].mmx_type != 20) |
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solvent.gpol[i] = -0.5*cc/(solvent.rsolv[i]+solvent.doffset+solvent.p1); |
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} |
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for (i=0; i < bonds_ff.nbnd; i++) |
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{ |
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it = bonds_ff.i12[i][0]; |
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kt = bonds_ff.i12[i][1]; |
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if (atom[it].mmx_type != 20 && atom[kt].mmx_type != 20) |
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{ |
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r = bonds_ff.bl[i]; |
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r4 = r*r*r*r; |
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solvent.gpol[it] += solvent.p2*solvent.vsolv[kt]/r4; |
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solvent.gpol[kt] += solvent.p2*solvent.vsolv[it]/r4; |
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} |
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} |
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for (i=0; i < angles.nang; i++) |
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{ |
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ia = angles.i13[i][0]; |
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ib = angles.i13[i][1]; |
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ic = angles.i13[i][2]; |
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if (atom[ia].mmx_type != 20 && atom[ib].mmx_type != 20 && atom[ic].mmx_type != 20) |
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{ |
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factor = 1.0; |
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for (j=0; j < MAXIAT; j++) |
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{ |
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if (atom[ia].iat[j] != 0) |
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{ |
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id = atom[ia].iat[j]; |
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if (id == ic) |
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factor = 0.0; |
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else if (id != ib) |
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{ |
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for (k=0; k < MAXIAT; k++) |
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{ |
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if (atom[ic].iat[k] != 0) |
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{ |
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if (atom[ic].iat[k] == id) |
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factor = 0.5; |
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} |
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} |
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} |
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} |
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} |
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id = find_bond(ia,ib); |
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rab = bonds_ff.bl[id]; |
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id = find_bond(ib,ic); |
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rbc = bonds_ff.bl[id]; |
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cosine = cos(angles.anat[i]/radian); |
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r2 = rab*rab + rbc*rbc - 2.0*rab*rbc*cosine; |
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r4 = r2*r2; |
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solvent.gpol[ia] += factor*solvent.p3*solvent.vsolv[ic]/r4; |
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solvent.gpol[ic] += factor*solvent.p3*solvent.vsolv[ia]/r4; |
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} |
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} |
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} |
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} |
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/* =================================================== */ |
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void born() |
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{ |
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int i,k; |
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double cc; |
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double ratio; |
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double xi,yi,zi,ri; |
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double rk,sk,sk2,sum; |
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double lik,lik2,uik,uik2; |
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double xr,yr,zr,rvdw; |
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double r,r2,r4; |
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double gpi,pip5,p5inv; |
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double theta,term,ccf; |
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cc = 4.80298*4.80298*14.39418; |
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if (solvent.type == STILL) |
| 281 |
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{ |
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p5inv = 1.0/solvent.p5; |
| 283 |
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pip5 = PI*solvent.p5; |
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for (i=1; i <= natom; i++) |
| 285 |
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{ |
| 286 |
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if (atom[i].mmx_type != 20) |
| 287 |
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{ |
| 288 |
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xi = atom[i].x; |
| 289 |
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yi = atom[i].y; |
| 290 |
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zi = atom[i].z; |
| 291 |
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gpi = solvent.gpol[i]; |
| 292 |
wdelano |
99 |
skip[i][i] = i; |
| 293 |
wdelano |
58 |
for (k = 1; k <= natom; k++) |
| 294 |
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{ |
| 295 |
wdelano |
99 |
if (skip[i][k] != i && atom[k].mmx_type != 20) |
| 296 |
wdelano |
58 |
{ |
| 297 |
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xr = atom[k].x - xi; |
| 298 |
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yr = atom[k].y - yi; |
| 299 |
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zr = atom[k].z - zi; |
| 300 |
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r2 = xr*xr + yr*yr + zr*zr; |
| 301 |
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r4 = r2*r2; |
| 302 |
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rvdw = solvent.rsolv[i] + solvent.rsolv[k]; |
| 303 |
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ratio = r2/(rvdw*rvdw); |
| 304 |
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if (ratio > p5inv) |
| 305 |
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{ |
| 306 |
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ccf = 1.0; |
| 307 |
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} else |
| 308 |
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{ |
| 309 |
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theta = ratio*pip5; |
| 310 |
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term = 0.5*(1.0-cos(theta)); |
| 311 |
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ccf = term*term; |
| 312 |
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} |
| 313 |
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gpi += solvent.p4*ccf*solvent.vsolv[k]/r4; |
| 314 |
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} |
| 315 |
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} |
| 316 |
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solvent.rborn[i] = -0.5*cc/gpi; |
| 317 |
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} |
| 318 |
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} |
| 319 |
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}else if (solvent.type == HCT) |
| 320 |
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{ |
| 321 |
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for (i=1; i <= natom; i++) |
| 322 |
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{ |
| 323 |
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if (atom[i].mmx_type != 20) |
| 324 |
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{ |
| 325 |
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xi = atom[i].x; |
| 326 |
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yi = atom[i].y; |
| 327 |
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zi = atom[i].z; |
| 328 |
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ri = solvent.rsolv[i] + solvent.doffset; |
| 329 |
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sum = 1.0/ri; |
| 330 |
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for (k=1; k <= natom; k++) |
| 331 |
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{ |
| 332 |
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if (i != k && atom[k].mmx_type != 20) |
| 333 |
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{ |
| 334 |
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xr = atom[k].x - xi; |
| 335 |
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yr = atom[k].y - yi; |
| 336 |
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zr = atom[k].z - zi; |
| 337 |
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r2 = xr*xr + yr*yr + zr*zr; |
| 338 |
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r = sqrt(r2); |
| 339 |
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rk = solvent.rsolv[k]+solvent.doffset; |
| 340 |
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sk = rk * solvent.shct[k]; |
| 341 |
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sk2 = sk*sk; |
| 342 |
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if (ri < (r+sk)) |
| 343 |
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{ |
| 344 |
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lik = 1.0/ MaxFun(ri,r-sk); |
| 345 |
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uik = 1.0/(r+sk); |
| 346 |
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lik2 = lik*lik; |
| 347 |
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uik2 = uik*uik; |
| 348 |
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term = lik - uik + 0.25*r*(uik2-lik2) + (0.5/r)*log(uik/lik) |
| 349 |
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+ (0.25*sk2/r)*(lik2-uik2); |
| 350 |
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sum -= 0.5*term; |
| 351 |
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|
} |
| 352 |
|
|
} |
| 353 |
|
|
} |
| 354 |
|
|
theta = 1.0/sum; |
| 355 |
|
|
solvent.rborn[i] = MaxFun(ri,theta); |
| 356 |
|
|
} |
| 357 |
|
|
} |
| 358 |
|
|
} |
| 359 |
|
|
} |
| 360 |
|
|
|
| 361 |
|
|
|
| 362 |
|
|
|
| 363 |
|
|
|
| 364 |
|
|
|
