| 1 |
#define EXTERN extern |
| 2 |
|
| 3 |
#include "pcwin.h" |
| 4 |
#include "pcmod.h" |
| 5 |
#include "bonds_ff.h" |
| 6 |
#include "angles.h" |
| 7 |
#include "field.h" |
| 8 |
#include "attached.h" |
| 9 |
|
| 10 |
#define STILL 1 |
| 11 |
#define HCT 2 |
| 12 |
|
| 13 |
EXTERN struct t_solvent { |
| 14 |
int type; |
| 15 |
double EPSin, EPSsolv; |
| 16 |
double doffset, p1,p2,p3,p4,p5; |
| 17 |
double *shct,*asolv,*rsolv,*vsolv,*gpol,*rborn; |
| 18 |
} solvent; |
| 19 |
|
| 20 |
|
| 21 |
int find_bond(int,int); |
| 22 |
void born(void); |
| 23 |
void ksolv(void); |
| 24 |
void message_alert(char *, char *); |
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|
| 26 |
// choices are gbsa models: Analytical Still and HCT |
| 27 |
// allocate memory in get_mem |
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|
| 29 |
void ksolv() |
| 30 |
{ |
| 31 |
int i,j,k, jji,it,kt; |
| 32 |
int ia,ib,ic,id; |
| 33 |
double ri,ri2,rk,cc; |
| 34 |
double r,r2,r4,rab,rbc; |
| 35 |
double cosine,factor; |
| 36 |
double h,ratio,term; |
| 37 |
|
| 38 |
solvent.doffset = -0.09; |
| 39 |
solvent.p1 = 0.073; |
| 40 |
solvent.p2 = 0.921; |
| 41 |
solvent.p3 = 6.211; |
| 42 |
solvent.p4 = 15.236; |
| 43 |
solvent.p5 = 1.254; |
| 44 |
|
| 45 |
if (solvent.type == HCT) |
| 46 |
{ |
| 47 |
for (i=1; i <= natom; i++) |
| 48 |
{ |
| 49 |
solvent.asolv[i] = 0.0054; |
| 50 |
solvent.shct[i] = 0.0; |
| 51 |
if (atom[i].atomnum == 1) solvent.shct[i] = 0.85; |
| 52 |
if (atom[i].mmx_type == 20) solvent.shct[i] = 0.85; |
| 53 |
if (atom[i].atomnum == 6) solvent.shct[i] = 0.72; |
| 54 |
if (atom[i].atomnum == 7) solvent.shct[i] = 0.79; |
| 55 |
if (atom[i].atomnum == 8) solvent.shct[i] = 0.85; |
| 56 |
if (atom[i].atomnum == 9) solvent.shct[i] = 0.88; |
| 57 |
if (atom[i].atomnum == 15) solvent.shct[i] = 0.86; |
| 58 |
if (atom[i].atomnum == 16) solvent.shct[i] = 0.96; |
| 59 |
if (atom[i].atomnum == 26) solvent.shct[i] = 0.88; |
| 60 |
} |
| 61 |
} else if (solvent.type == STILL) |
| 62 |
{ |
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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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} |
| 67 |
} |
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// assign standard radii |
| 69 |
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; |
| 76 |
if (atom[atom[i].iat[0]].atomnum == 8) solvent.rsolv[i] = 1.05; |
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} else if (atom[i].mmx_type == 20) |
| 78 |
{ |
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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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|
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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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|
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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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|
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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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} |
| 221 |
} |
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|
| 223 |
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]; |
| 227 |
ic = angles.i13[i][2]; |
| 228 |
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++) |
| 232 |
{ |
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if (atom[ia].iat[j] != 0) |
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{ |
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id = atom[ia].iat[j]; |
| 236 |
if (id == ic) |
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factor = 0.0; |
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else if (id != ib) |
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{ |
| 240 |
for (k=0; k < MAXIAT; k++) |
| 241 |
{ |
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if (atom[ic].iat[k] != 0) |
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{ |
| 244 |
if (atom[ic].iat[k] == id) |
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factor = 0.5; |
| 246 |
} |
| 247 |
} |
| 248 |
} |
| 249 |
} |
| 250 |
} |
| 251 |
|
| 252 |
id = find_bond(ia,ib); |
| 253 |
rab = bonds_ff.bl[id]; |
| 254 |
id = find_bond(ib,ic); |
| 255 |
rbc = bonds_ff.bl[id]; |
| 256 |
cosine = cos(angles.anat[i]/radian); |
| 257 |
r2 = rab*rab + rbc*rbc - 2.0*rab*rbc*cosine; |
| 258 |
r4 = r2*r2; |
| 259 |
solvent.gpol[ia] += factor*solvent.p3*solvent.vsolv[ic]/r4; |
| 260 |
solvent.gpol[ic] += factor*solvent.p3*solvent.vsolv[ia]/r4; |
| 261 |
} |
| 262 |
} |
| 263 |
} |
| 264 |
} |
| 265 |
/* =================================================== */ |
| 266 |
void born() |
| 267 |
{ |
| 268 |
int i,k; |
| 269 |
double cc; |
| 270 |
double ratio; |
| 271 |
double xi,yi,zi,ri; |
| 272 |
double rk,sk,sk2,sum; |
| 273 |
double lik,lik2,uik,uik2; |
| 274 |
double xr,yr,zr,rvdw; |
| 275 |
double r,r2,r4; |
| 276 |
double gpi,pip5,p5inv; |
| 277 |
double theta,term,ccf; |
| 278 |
|
| 279 |
cc = 4.80298*4.80298*14.39418; |
| 280 |
if (solvent.type == STILL) |
| 281 |
{ |
| 282 |
p5inv = 1.0/solvent.p5; |
| 283 |
pip5 = PI*solvent.p5; |
| 284 |
for (i=1; i <= natom; i++) |
| 285 |
{ |
| 286 |
if (atom[i].mmx_type != 20) |
| 287 |
{ |
| 288 |
xi = atom[i].x; |
| 289 |
yi = atom[i].y; |
| 290 |
zi = atom[i].z; |
| 291 |
gpi = solvent.gpol[i]; |
| 292 |
skip[i][i] = i; |
| 293 |
for (k = 1; k <= natom; k++) |
| 294 |
{ |
| 295 |
if (skip[i][k] != i && atom[k].mmx_type != 20) |
| 296 |
{ |
| 297 |
xr = atom[k].x - xi; |
| 298 |
yr = atom[k].y - yi; |
| 299 |
zr = atom[k].z - zi; |
| 300 |
r2 = xr*xr + yr*yr + zr*zr; |
| 301 |
r4 = r2*r2; |
| 302 |
rvdw = solvent.rsolv[i] + solvent.rsolv[k]; |
| 303 |
ratio = r2/(rvdw*rvdw); |
| 304 |
if (ratio > p5inv) |
| 305 |
{ |
| 306 |
ccf = 1.0; |
| 307 |
} else |
| 308 |
{ |
| 309 |
theta = ratio*pip5; |
| 310 |
term = 0.5*(1.0-cos(theta)); |
| 311 |
ccf = term*term; |
| 312 |
} |
| 313 |
gpi += solvent.p4*ccf*solvent.vsolv[k]/r4; |
| 314 |
} |
| 315 |
} |
| 316 |
solvent.rborn[i] = -0.5*cc/gpi; |
| 317 |
} |
| 318 |
} |
| 319 |
}else if (solvent.type == HCT) |
| 320 |
{ |
| 321 |
for (i=1; i <= natom; i++) |
| 322 |
{ |
| 323 |
if (atom[i].mmx_type != 20) |
| 324 |
{ |
| 325 |
xi = atom[i].x; |
| 326 |
yi = atom[i].y; |
| 327 |
zi = atom[i].z; |
| 328 |
ri = solvent.rsolv[i] + solvent.doffset; |
| 329 |
sum = 1.0/ri; |
| 330 |
for (k=1; k <= natom; k++) |
| 331 |
{ |
| 332 |
if (i != k && atom[k].mmx_type != 20) |
| 333 |
{ |
| 334 |
xr = atom[k].x - xi; |
| 335 |
yr = atom[k].y - yi; |
| 336 |
zr = atom[k].z - zi; |
| 337 |
r2 = xr*xr + yr*yr + zr*zr; |
| 338 |
r = sqrt(r2); |
| 339 |
rk = solvent.rsolv[k]+solvent.doffset; |
| 340 |
sk = rk * solvent.shct[k]; |
| 341 |
sk2 = sk*sk; |
| 342 |
if (ri < (r+sk)) |
| 343 |
{ |
| 344 |
lik = 1.0/ MaxFun(ri,r-sk); |
| 345 |
uik = 1.0/(r+sk); |
| 346 |
lik2 = lik*lik; |
| 347 |
uik2 = uik*uik; |
| 348 |
term = lik - uik + 0.25*r*(uik2-lik2) + (0.5/r)*log(uik/lik) |
| 349 |
+ (0.25*sk2/r)*(lik2-uik2); |
| 350 |
sum -= 0.5*term; |
| 351 |
} |
| 352 |
} |
| 353 |
} |
| 354 |
theta = 1.0/sum; |
| 355 |
solvent.rborn[i] = MaxFun(ri,theta); |
| 356 |
} |
| 357 |
} |
| 358 |
} |
| 359 |
} |
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|
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|
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|
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|
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