| 1 |
#define EXTERN extern |
| 2 |
#include "pcwin.h" |
| 3 |
#include "pcmod.h" |
| 4 |
#include "nonbond.h" |
| 5 |
#include "pot.h" |
| 6 |
#include "field.h" |
| 7 |
#include "atom_k.h" |
| 8 |
|
| 9 |
void numeral(int,char *,int); |
| 10 |
|
| 11 |
EXTERN struct t_vdw1 { |
| 12 |
int nvdw; |
| 13 |
float rad[MAXVDWCONST], eps[MAXVDWCONST]; |
| 14 |
int lpd[MAXVDWCONST], ihtyp[MAXVDWCONST], ihdon[MAXVDWCONST]; |
| 15 |
float alpha[MAXVDWCONST],n[MAXVDWCONST],a[MAXVDWCONST],g[MAXVDWCONST]; |
| 16 |
char da[MAXVDWCONST][2]; |
| 17 |
} vdw1; |
| 18 |
|
| 19 |
EXTERN struct t_vdwpr_k { |
| 20 |
int nvdwpr; |
| 21 |
int ia1[MAXBONDCONST],ia2[MAXBONDCONST]; |
| 22 |
char kv[MAXBONDCONST][7]; |
| 23 |
float radius[MAXBONDCONST], eps[MAXBONDCONST]; |
| 24 |
} vdwpr_k; |
| 25 |
|
| 26 |
struct t_mm3hbond { |
| 27 |
int npair; |
| 28 |
int htype[MAXBONDCONST]; |
| 29 |
int otype[MAXBONDCONST]; |
| 30 |
} mm3hbond; |
| 31 |
|
| 32 |
EXTERN int Missing_constants; |
| 33 |
|
| 34 |
void kvdw() |
| 35 |
{ |
| 36 |
int i, j, k; |
| 37 |
int it, ita, itb, found, ianum,ibnum; |
| 38 |
int dapair; |
| 39 |
char pa[4],pb[4],pt[7]; |
| 40 |
long int hbmask; |
| 41 |
float rad_ia, rad_ib; |
| 42 |
float eps1, eps2, seps1, seps2; |
| 43 |
float rii,rjj,gammaij, rij, epsij; |
| 44 |
|
| 45 |
// mm3 setup |
| 46 |
if (field.type == MM3) |
| 47 |
{ |
| 48 |
mm3hbond.npair = 0; |
| 49 |
for (i=0; i < vdwpr_k.nvdwpr; i++) |
| 50 |
{ |
| 51 |
if (atom_k.number[vdwpr_k.ia1[i]] == 1) // looking for hydrogens |
| 52 |
{ |
| 53 |
mm3hbond.htype[mm3hbond.npair] = vdwpr_k.ia1[i]; |
| 54 |
mm3hbond.otype[mm3hbond.npair] = vdwpr_k.ia2[i]; |
| 55 |
mm3hbond.npair++; |
| 56 |
} else if (atom_k.number[vdwpr_k.ia2[i]] == 1) |
| 57 |
{ |
| 58 |
if (!( (vdwpr_k.ia2[i] == 5 && vdwpr_k.ia1[i] == 1) || (vdwpr_k.ia2[i] == 36 && vdwpr_k.ia1[i] == 1) )) |
| 59 |
{ |
| 60 |
mm3hbond.htype[mm3hbond.npair] = vdwpr_k.ia2[i]; |
| 61 |
mm3hbond.otype[mm3hbond.npair] = vdwpr_k.ia1[i]; |
| 62 |
mm3hbond.npair++; |
| 63 |
} |
| 64 |
} |
| 65 |
} |
| 66 |
} |
| 67 |
// |
| 68 |
nonbond.npair = 0; |
| 69 |
hbmask = 1 << HBOND_MASK; |
| 70 |
for (i=0; i <= nonbond.maxnbtype; i++) |
| 71 |
{ |
| 72 |
for (j=0; j <= nonbond.maxnbtype; j++) |
| 73 |
nonbond.iNBtype[j][i] = 0; |
| 74 |
} |
| 75 |
|
| 76 |
for (i=1; i < natom; i++) |
| 77 |
{ |
| 78 |
ita = atom[i].type; |
| 79 |
ianum = atom[i].atomnum; |
| 80 |
for (j= i+1; j <= natom; j++) |
| 81 |
{ |
| 82 |
itb = atom[j].type; |
| 83 |
ibnum = atom[j].atomnum; |
| 84 |
if (ita < itb) |
| 85 |
it = 1000*ita + itb; |
| 86 |
else |
| 87 |
it = 1000*itb + ita; |
| 88 |
|
| 89 |
found = FALSE; |
| 90 |
if (nonbond.iNBtype[ita][itb] != 0) |
| 91 |
found = TRUE; |
| 92 |
|
| 93 |
if (found == FALSE) |
| 94 |
{ |
| 95 |
if (field.type == MMFF94) |
| 96 |
{ |
| 97 |
dapair = FALSE; |
| 98 |
rii = vdw1.a[ita]*pow(vdw1.alpha[ita],0.25); |
| 99 |
rjj = vdw1.a[itb]*pow(vdw1.alpha[itb],0.25); |
| 100 |
if ((atom[i].atomnum == 1 && ita != 5) || (atom[j].atomnum ==1 && itb != 5) ) // polar hydrogens |
| 101 |
{ |
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rij = 0.5*(rii+rjj); |
| 103 |
if ( (strcmp(vdw1.da[ita],"A") == 0) && (strcmp(vdw1.da[itb],"D") == 0) ) |
| 104 |
{ |
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dapair = TRUE; |
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} |
| 107 |
if ( (strcmp(vdw1.da[itb],"A") == 0) && (strcmp(vdw1.da[ita],"D") == 0) ) |
| 108 |
{ |
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dapair = TRUE; |
| 110 |
} |
| 111 |
} else |
| 112 |
{ |
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gammaij = (rii-rjj)/(rii+rjj); |
| 114 |
rij = 0.5*(rii+rjj)*(1.00+0.2*(1.00- exp(-12.0*gammaij*gammaij))); |
| 115 |
} |
| 116 |
epsij = ((181.16*vdw1.g[ita]*vdw1.g[itb]*vdw1.alpha[ita]*vdw1.alpha[itb])/ |
| 117 |
( sqrt(vdw1.alpha[ita]/vdw1.n[ita]) + sqrt(vdw1.alpha[itb]/vdw1.n[itb])) ) / pow(rij,6.0); |
| 118 |
|
| 119 |
if (dapair == TRUE) |
| 120 |
{ |
| 121 |
rij *= 0.8; |
| 122 |
epsij *= 0.5; |
| 123 |
} |
| 124 |
|
| 125 |
nonbond.vrad[ita][itb] = rij; |
| 126 |
nonbond.veps[ita][itb] = epsij; |
| 127 |
nonbond.ipif[ita][itb] = 1.0; |
| 128 |
nonbond.vrad[itb][ita] = rij; |
| 129 |
nonbond.veps[itb][ita] = epsij; |
| 130 |
nonbond.ipif[itb][ita] = 1.0; |
| 131 |
|
| 132 |
nonbond.vrad14[ita][itb] = nonbond.vrad[ita][itb]; |
| 133 |
nonbond.vrad14[itb][ita] = nonbond.vrad[itb][ita]; |
| 134 |
nonbond.veps14[ita][itb] = nonbond.veps[ita][itb]; |
| 135 |
nonbond.veps14[itb][ita] = nonbond.veps[itb][ita]; |
| 136 |
|
| 137 |
} else |
| 138 |
{ |
| 139 |
rad_ia = vdw1.rad[ita]; |
| 140 |
rad_ib = vdw1.rad[itb]; |
| 141 |
if (strcmp(field.radiustype,"SIGMA") == 0) |
| 142 |
{ |
| 143 |
rad_ia *= 1.122462048; |
| 144 |
rad_ib *= 1.122462048; |
| 145 |
} |
| 146 |
if (strcmp(field.radiussize,"DIAMETER") == 0) |
| 147 |
{ |
| 148 |
rad_ia /= 2.0; |
| 149 |
rad_ib /= 2.0; |
| 150 |
} |
| 151 |
eps1 = vdw1.eps[ita]; |
| 152 |
eps2 = vdw1.eps[itb]; |
| 153 |
|
| 154 |
if (strcmp(field.radiusrule,"ARITHMETIC") == 0) |
| 155 |
{ |
| 156 |
nonbond.vrad[ita][itb] = rad_ia + rad_ib; |
| 157 |
nonbond.vrad[itb][ita] = rad_ia + rad_ib; |
| 158 |
} else if (strcmp(field.radiusrule,"GEOMETRIC") == 0) |
| 159 |
{ |
| 160 |
nonbond.vrad[ita][itb] = 2.0*( sqrt(rad_ia)*sqrt(rad_ib)); |
| 161 |
nonbond.vrad[itb][ita] = 2.0*( sqrt(rad_ia)*sqrt(rad_ib)); |
| 162 |
} else if (strcmp(field.radiusrule,"CUBIC-MEAN") == 0) |
| 163 |
{ |
| 164 |
if ((atom[i].atomnum == 1 && ita != 5) || (atom[j].atomnum ==1 && itb != 5) ) // polar hydrogens |
| 165 |
{ |
| 166 |
nonbond.vrad[ita][itb] = rad_ia + rad_ib; |
| 167 |
nonbond.vrad[itb][ita] = rad_ia + rad_ib; |
| 168 |
}else |
| 169 |
{ |
| 170 |
nonbond.vrad[ita][itb] = 2.0*( ((rad_ia*rad_ia*rad_ia) + (rad_ib*rad_ib*rad_ib))/(rad_ia*rad_ia + rad_ib*rad_ib) ); |
| 171 |
nonbond.vrad[itb][ita] = 2.0*( ((rad_ia*rad_ia*rad_ia) + (rad_ib*rad_ib*rad_ib))/(rad_ia*rad_ia + rad_ib*rad_ib) ); |
| 172 |
} |
| 173 |
} else |
| 174 |
{ |
| 175 |
nonbond.vrad[ita][itb] = rad_ia + rad_ib; |
| 176 |
nonbond.vrad[itb][ita] = rad_ia + rad_ib; |
| 177 |
} |
| 178 |
|
| 179 |
if (strcmp(field.epsrule,"ARITHMETIC") == 0) |
| 180 |
{ |
| 181 |
nonbond.veps[ita][itb] = 0.5*(eps1 + eps2); |
| 182 |
nonbond.veps[itb][ita] = 0.5*(eps1 + eps2); |
| 183 |
} else if (strcmp(field.epsrule,"GEOMETRIC") == 0) |
| 184 |
{ |
| 185 |
nonbond.veps[ita][itb] = sqrt( eps1*eps2 ); |
| 186 |
nonbond.veps[itb][ita] = sqrt( eps1*eps2 ); |
| 187 |
} else if (strcmp(field.epsrule,"HARMONIC") == 0) |
| 188 |
{ |
| 189 |
nonbond.veps[ita][itb] = 2.0* (eps1*eps2)/(eps1+eps2); |
| 190 |
nonbond.veps[itb][ita] = 2.0* (eps1*eps2)/(eps1+eps2); |
| 191 |
} else if (strcmp(field.epsrule,"HHG") == 0) |
| 192 |
{ |
| 193 |
if ((atom[i].atomnum == 1 && ita != 5) || (atom[j].atomnum ==1 && itb != 5) ) // polar hydrogens |
| 194 |
{ |
| 195 |
nonbond.veps[ita][itb] = 0.5*(eps1 + eps2); |
| 196 |
nonbond.veps[itb][ita] = 0.5*(eps1 + eps2); |
| 197 |
} else |
| 198 |
{ |
| 199 |
seps1 = sqrt(eps1); |
| 200 |
seps2 = sqrt(eps2); |
| 201 |
nonbond.veps[ita][itb] = 4.0*(eps1*eps2)/( (seps1+seps2)*(seps1+seps2)); |
| 202 |
nonbond.veps[itb][ita] = 4.0*(eps1*eps2)/( (seps1+seps2)*(seps1+seps2)); |
| 203 |
} |
| 204 |
}else |
| 205 |
{ |
| 206 |
nonbond.veps[ita][itb] = sqrt( eps1*eps2 ); |
| 207 |
nonbond.veps[itb][ita] = sqrt( eps1*eps2 ); |
| 208 |
} |
| 209 |
|
| 210 |
if (field.type == MM3) |
| 211 |
{ |
| 212 |
nonbond.ipif[ita][itb] = 1; |
| 213 |
nonbond.ipif[itb][ita] = 1; |
| 214 |
} else if (field.type == MMX) |
| 215 |
{ |
| 216 |
nonbond.ipif[ita][itb] = 1; |
| 217 |
nonbond.ipif[itb][ita] = 1; |
| 218 |
if( (ita == 2 || ita == 4 || ita == 40 || ita == 48) && |
| 219 |
(itb == 2 || itb == 4 || itb == 40 || itb == 48) ) |
| 220 |
{ |
| 221 |
nonbond.ipif[ita][itb] = 0; |
| 222 |
nonbond.ipif[itb][ita] = 0; |
| 223 |
} |
| 224 |
} |
| 225 |
nonbond.vrad14[ita][itb] = nonbond.vrad[ita][itb]; |
| 226 |
nonbond.vrad14[itb][ita] = nonbond.vrad[itb][ita]; |
| 227 |
nonbond.veps14[ita][itb] = nonbond.veps[ita][itb]; |
| 228 |
nonbond.veps14[itb][ita] = nonbond.veps[itb][ita]; |
| 229 |
} |
| 230 |
// look for any special vdw pairs |
| 231 |
numeral(atom[i].type,pa,3); |
| 232 |
numeral(atom[j].type,pb,3); |
| 233 |
|
| 234 |
if (atom[i].type < atom[j].type) |
| 235 |
{ |
| 236 |
strcpy(pt,pa); |
| 237 |
strcat(pt,pb); |
| 238 |
} else |
| 239 |
{ |
| 240 |
strcpy(pt,pb); |
| 241 |
strcat(pt,pa); |
| 242 |
} |
| 243 |
|
| 244 |
// look for vdw pairs |
| 245 |
for (k= 0; k < vdwpr_k.nvdwpr ; k++) |
| 246 |
{ |
| 247 |
if (strcmp(vdwpr_k.kv[k],pt) == 0) |
| 248 |
{ |
| 249 |
nonbond.vrad[ita][itb] = vdwpr_k.radius[k]; |
| 250 |
nonbond.vrad[itb][ita] = vdwpr_k.radius[k]; |
| 251 |
nonbond.veps[ita][itb] = vdwpr_k.eps[k]; |
| 252 |
nonbond.veps[itb][ita] = vdwpr_k.eps[k]; |
| 253 |
if (ianum != 1 && ibnum != 1 ) |
| 254 |
{ |
| 255 |
nonbond.veps[ita][itb] /= units.dielec; |
| 256 |
nonbond.veps[itb][ita] /= units.dielec; |
| 257 |
} |
| 258 |
if (ita == 1 && itb == 5) |
| 259 |
{ |
| 260 |
nonbond.vrad14[ita][itb] = nonbond.vrad[ita][itb]; |
| 261 |
nonbond.vrad14[itb][ita] = nonbond.vrad[itb][ita]; |
| 262 |
nonbond.veps14[itb][ita] = nonbond.veps[itb][ita]; |
| 263 |
nonbond.veps14[ita][itb] = nonbond.veps[ita][itb]; |
| 264 |
} |
| 265 |
break; |
| 266 |
} |
| 267 |
} |
| 268 |
|
| 269 |
nonbond.iNBtype[ita][itb] = it; |
| 270 |
nonbond.iNBtype[itb][ita] = it; |
| 271 |
|
| 272 |
if (pot.use_hbond) |
| 273 |
{ |
| 274 |
if ( atom[i].flags & hbmask || atom[i].mmx_type == 20) |
| 275 |
{ |
| 276 |
for (k=0; k < MAXIAT; k++) |
| 277 |
{ |
| 278 |
if (atom[j].iat[k] != 0 && atom[j].bo[k] != 9) |
| 279 |
{ |
| 280 |
if (atom[atom[j].iat[k]].flags & hbmask || atom[atom[j].iat[k]].mmx_type == 20) |
| 281 |
{ |
| 282 |
nonbond.vrad[ita][itb] -= 0.25; |
| 283 |
nonbond.vrad[itb][ita] -= 0.25; |
| 284 |
break; |
| 285 |
} |
| 286 |
} |
| 287 |
} |
| 288 |
} else if (atom[j].flags & hbmask || atom[j].mmx_type == 20) |
| 289 |
{ |
| 290 |
for (k=0; k < MAXIAT; k++) |
| 291 |
{ |
| 292 |
if (atom[i].iat[k] != 0 && atom[i].bo[k] != 9) |
| 293 |
{ |
| 294 |
if (atom[atom[i].iat[k]].flags & hbmask || atom[atom[i].iat[k]].mmx_type == 20) |
| 295 |
{ |
| 296 |
nonbond.vrad[ita][itb] -= 0.25; |
| 297 |
nonbond.vrad[itb][ita] -= 0.25; |
| 298 |
break; |
| 299 |
} |
| 300 |
} |
| 301 |
} |
| 302 |
} |
| 303 |
} |
| 304 |
nonbond.npair++; |
| 305 |
} |
| 306 |
} |
| 307 |
} |
| 308 |
for (i=1; i <= natom ; i++) |
| 309 |
{ |
| 310 |
ita = atom[i].type; |
| 311 |
if (vdw1.rad[ita] == 0) |
| 312 |
{ |
| 313 |
rii = vdw1.a[ita]*pow(vdw1.alpha[ita],0.25); |
| 314 |
vdw1.rad[ita] = 0.5*rii; |
| 315 |
} |
| 316 |
} |
| 317 |
} |
