| 3 |
|
#include "pcwin.h" |
| 4 |
|
#include "pcmod.h" |
| 5 |
|
|
| 6 |
< |
#include "angles.h" |
| 7 |
< |
|
| 6 |
> |
#include "attached.h" |
| 7 |
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#include "energies.h" |
| 9 |
– |
#include "rings.h" |
| 10 |
– |
#include "torsions.h" |
| 8 |
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#include "bonds_ff.h" |
| 9 |
|
#include "derivs.h" |
| 13 |
– |
#include "hess.h" |
| 10 |
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#include "pot.h" |
| 15 |
– |
#include "gmmx.h" |
| 11 |
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#include "utility.h" |
| 12 |
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#include "solv.h" |
| 18 |
– |
#include "field.h" |
| 13 |
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#include "dipmom.h" |
| 14 |
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|
| 21 |
– |
struct t_cbonds { |
| 22 |
– |
int nbnd, icbonds[MAXCBND][3], lpd[MAXCBND], ia1[MAXCBND],ia2[MAXCBND]; |
| 23 |
– |
double vrad[MAXCBND],veps[MAXCBND]; |
| 24 |
– |
} cbonds; |
| 25 |
– |
EXTERN struct t_high_coord { |
| 26 |
– |
int ncoord, i13[400][3]; |
| 27 |
– |
} high_coord; |
| 28 |
– |
|
| 15 |
|
EXTERN struct t_minim_control { |
| 16 |
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int type, method, field, added_const; |
| 17 |
|
char added_path[256],added_name[256]; |
| 28 |
|
} solvent; |
| 29 |
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|
| 30 |
|
int Missing_constants; |
| 45 |
– |
FILE *errfile; |
| 31 |
|
|
| 47 |
– |
FILE * fopen_path ( char * , char * , char * ) ; |
| 32 |
|
void message_alert(char *,char *); |
| 49 |
– |
void get_added_const(void); |
| 50 |
– |
void assign_gast_charge(); |
| 51 |
– |
void lattice(void); |
| 52 |
– |
void bounds(void); |
| 33 |
|
void pcm7_min(void); |
| 54 |
– |
int iscoord_bond(int, int); |
| 55 |
– |
void get_coordbonds(void); |
| 34 |
|
int isbond(int, int); |
| 57 |
– |
int ishbond(int, int); |
| 58 |
– |
int istorsion(int, int); |
| 59 |
– |
void get_hbond(void); |
| 60 |
– |
void mark_hbond(void); |
| 61 |
– |
void reset_atom_data(void); |
| 35 |
|
int initialise(void); |
| 36 |
|
void get_bonds(void); |
| 37 |
|
void get_torsions(void); |
| 40 |
|
double energy(void); |
| 41 |
|
double print_energy(void); |
| 42 |
|
void pcmfout(int); |
| 70 |
– |
void orbital(void); |
| 71 |
– |
void free_orbit(void); |
| 43 |
|
void set_active(void); |
| 44 |
< |
void estrtor(void); |
| 45 |
< |
void echarge(void); |
| 46 |
< |
void ewald(void); |
| 47 |
< |
void eurey(void); |
| 48 |
< |
void ebuck(void); |
| 49 |
< |
void ebuckmm3(void); |
| 44 |
> |
int setup_calculation(void); |
| 45 |
> |
void end_calculation(void); |
| 46 |
> |
|
| 47 |
> |
void egeom1(void); |
| 48 |
> |
void esolv1(void); |
| 49 |
> |
void egeom(void); |
| 50 |
> |
void esolv(void); |
| 51 |
> |
|
| 52 |
> |
void ehal(void); |
| 53 |
> |
void ehal1(void); |
| 54 |
> |
void ebufcharge(void); |
| 55 |
> |
void ebufcharge1(void); |
| 56 |
> |
void eopbend_wilson(void); |
| 57 |
> |
void eopbend_wilson1(void); |
| 58 |
> |
|
| 59 |
|
void estrbnd(void); |
| 80 |
– |
void edipole(void); |
| 60 |
|
void etorsion(void); |
| 61 |
|
void eangang(void); |
| 62 |
|
void eangle(void); |
| 63 |
|
void ebond(void); |
| 64 |
< |
void eopbend(void); |
| 86 |
< |
void ehbond(void); |
| 87 |
< |
void eimprop(void); |
| 88 |
< |
void eimptors(void); |
| 89 |
< |
void elj(void); |
| 90 |
< |
void ecoord_bond(void); |
| 91 |
< |
void elj_qq(void); |
| 92 |
< |
void ebuck_charge(void); |
| 93 |
< |
void ehigh_coord(void); |
| 94 |
< |
|
| 95 |
< |
void estrtor1(void); |
| 96 |
< |
void echarge1(void); |
| 97 |
< |
void ebuck1(void); |
| 98 |
< |
void ebuckmm31(void); |
| 64 |
> |
|
| 65 |
|
void estrbnd1(void); |
| 100 |
– |
void edipole1(void); |
| 66 |
|
void etorsion1(void); |
| 102 |
– |
void eangang1(void); |
| 67 |
|
void eangle1(void); |
| 68 |
|
void ebond1(void); |
| 105 |
– |
void eopbend1(void); |
| 106 |
– |
void ehbond1(void); |
| 107 |
– |
void eimprop1(void); |
| 108 |
– |
void eimptors1(void); |
| 109 |
– |
void elj1(void); |
| 110 |
– |
void ecoord_bond1(void); |
| 111 |
– |
void ewald1(void); |
| 112 |
– |
void eurey1(void); |
| 113 |
– |
void elj_qq1(void); |
| 114 |
– |
void ebuck_charge1(void); |
| 115 |
– |
void ehigh_coord1(void); |
| 69 |
|
|
| 70 |
|
void kangle(void); |
| 118 |
– |
void korbit(void); |
| 71 |
|
void ktorsion(void); |
| 120 |
– |
void kdipole(void); |
| 72 |
|
void kstrbnd(void); |
| 73 |
|
void kcharge(void); |
| 74 |
|
void ksolv(void); |
| 124 |
– |
void kangang(void); |
| 75 |
|
void kopbend(void); |
| 126 |
– |
void kstrtor(void); |
| 127 |
– |
void khbond(void); |
| 128 |
– |
void piseq(int, int); |
| 129 |
– |
void kimprop(void); |
| 130 |
– |
void kimptors(void); |
| 131 |
– |
void kcoord_bonds(void); |
| 76 |
|
void kvdw(void); |
| 77 |
|
int kbond(void); |
| 134 |
– |
void kewald(void); |
| 135 |
– |
void kurey(void); |
| 78 |
|
|
| 79 |
|
void get_memory(void); |
| 80 |
|
void free_memory(void); |
| 81 |
|
void gradient(void); |
| 82 |
|
void minimize(void); |
| 141 |
– |
void dynamics(void); |
| 83 |
|
void read_datafiles(char *); |
| 84 |
+ |
void get_added_const(void); |
| 85 |
|
void attach(void); |
| 144 |
– |
void eheat(void); |
| 145 |
– |
void pirite(void); |
| 146 |
– |
void piden(void); |
| 86 |
|
void hdel(int); |
| 87 |
|
void set_atomtypes(int); |
| 88 |
|
void type(void); |
| 150 |
– |
void generate_bonds(void); |
| 89 |
|
void zero_data(void); |
| 152 |
– |
void ehal(void); |
| 153 |
– |
void ehal1(void); |
| 154 |
– |
void ebufcharge(void); |
| 155 |
– |
void ebufcharge1(void); |
| 156 |
– |
void eopbend_wilson(void); |
| 157 |
– |
void eopbend_wilson1(void); |
| 158 |
– |
void hbondreset(void); |
| 159 |
– |
void vibrate(void); |
| 160 |
– |
void pireset(void); |
| 161 |
– |
void adjust_mmfftypes(void); |
| 162 |
– |
void build_neighbor_list(int); |
| 163 |
– |
int setup_calculation(void); |
| 164 |
– |
void end_calculation(void); |
| 165 |
– |
void egeom1(void); |
| 166 |
– |
void esolv1(void); |
| 167 |
– |
void egeom(void); |
| 168 |
– |
void esolv(void); |
| 90 |
|
void xlogp(float *); |
| 91 |
|
|
| 171 |
– |
void mmxsub(int ia) |
| 172 |
– |
{ |
| 173 |
– |
int nret; |
| 174 |
– |
|
| 175 |
– |
minim_control.type = ia; // 0 to minimize, 1 for single point |
| 176 |
– |
nret = setup_calculation(); |
| 177 |
– |
if (nret == FALSE) |
| 178 |
– |
{ |
| 179 |
– |
end_calculation(); |
| 180 |
– |
return; |
| 181 |
– |
} |
| 182 |
– |
|
| 183 |
– |
pcm7_min(); |
| 184 |
– |
end_calculation(); |
| 185 |
– |
} |
| 186 |
– |
// ================================================================ |
| 187 |
– |
void pcm7_min() |
| 188 |
– |
{ |
| 189 |
– |
int i, print; |
| 190 |
– |
double etot; |
| 191 |
– |
|
| 192 |
– |
print = FALSE; |
| 193 |
– |
if (minim_values.iprint == TRUE) |
| 194 |
– |
{ |
| 195 |
– |
print = TRUE; |
| 196 |
– |
minim_values.iprint = FALSE; |
| 197 |
– |
} |
| 198 |
– |
|
| 199 |
– |
if (minim_control.type == 1) // single point calculation |
| 200 |
– |
return; |
| 201 |
– |
|
| 202 |
– |
minimize(); |
| 203 |
– |
|
| 204 |
– |
if (print == TRUE) |
| 205 |
– |
minim_values.iprint = TRUE; |
| 206 |
– |
|
| 207 |
– |
if (minim_values.iprint == TRUE) |
| 208 |
– |
etot = print_energy(); |
| 209 |
– |
else |
| 210 |
– |
etot = energy(); |
| 211 |
– |
|
| 212 |
– |
// compute dipole moment here |
| 213 |
– |
dipolemom.xdipole = 0.0; |
| 214 |
– |
dipolemom.ydipole = 0.0; |
| 215 |
– |
dipolemom.zdipole = 0.0; |
| 216 |
– |
if (pot.use_charge || pot.use_bufcharge) charge_dipole(); |
| 217 |
– |
if (pot.use_dipole) dipole_dipole(); |
| 218 |
– |
dipolemom.total = sqrt(dipolemom.xdipole*dipolemom.xdipole + |
| 219 |
– |
dipolemom.ydipole*dipolemom.ydipole + |
| 220 |
– |
dipolemom.zdipole*dipolemom.zdipole); |
| 221 |
– |
} |
| 92 |
|
// ================================================================== |
| 93 |
|
int setup_calculation() |
| 94 |
|
{ |
| 95 |
< |
int nRet; |
| 95 |
> |
int i,j,nRet; |
| 96 |
|
char string[30]; |
| 97 |
|
double etot; |
| 98 |
< |
if (minim_control.field == MM3) |
| 229 |
< |
{ |
| 230 |
< |
// copy mm3 types into type file and retype |
| 231 |
< |
pot.use_hbond = FALSE; |
| 232 |
< |
hbondreset(); |
| 233 |
< |
hdel(1); |
| 234 |
< |
strcpy(string,"mm3.prm"); |
| 235 |
< |
zero_data(); |
| 236 |
< |
read_datafiles(string); |
| 237 |
< |
set_field(); |
| 238 |
< |
default_intype = MM3; |
| 239 |
< |
default_outtype = MM3; |
| 240 |
< |
set_atomtypes(MM3); |
| 241 |
< |
generate_bonds(); |
| 242 |
< |
if (minim_control.added_const) |
| 243 |
< |
get_added_const(); |
| 244 |
< |
} else if (minim_control.field == MMFF94) |
| 98 |
> |
if (minim_control.field == MMFF94) |
| 99 |
|
{ |
| 100 |
|
// copy mm3 types into type file and retype |
| 101 |
|
pot.use_hbond = FALSE; |
| 102 |
|
pot.use_picalc = FALSE; |
| 249 |
– |
hbondreset(); |
| 250 |
– |
pireset(); |
| 103 |
|
hdel(1); |
| 104 |
|
set_field(); |
| 253 |
– |
default_intype = MMFF94; |
| 254 |
– |
default_outtype = MMFF94; |
| 105 |
|
set_atomtypes(MMFF94); |
| 256 |
– |
generate_bonds(); |
| 257 |
– |
if (minim_control.added_const) |
| 258 |
– |
get_added_const(); |
| 259 |
– |
} else if (minim_control.field == AMBER) |
| 260 |
– |
{ |
| 261 |
– |
pot.use_hbond = FALSE; |
| 262 |
– |
pot.use_picalc = FALSE; |
| 263 |
– |
hbondreset(); |
| 264 |
– |
pireset(); |
| 265 |
– |
hdel(2); |
| 266 |
– |
set_field(); |
| 267 |
– |
generate_bonds(); |
| 268 |
– |
if (minim_control.added_const) |
| 269 |
– |
get_added_const(); |
| 270 |
– |
} else if (minim_control.field == OPLSAA) |
| 271 |
– |
{ |
| 272 |
– |
pot.use_hbond = FALSE; |
| 273 |
– |
pot.use_picalc = FALSE; |
| 274 |
– |
hbondreset(); |
| 275 |
– |
pireset(); |
| 276 |
– |
hdel(1); |
| 277 |
– |
set_field(); |
| 278 |
– |
generate_bonds(); |
| 106 |
|
if (minim_control.added_const) |
| 107 |
|
get_added_const(); |
| 108 |
|
} else |
| 116 |
|
} |
| 117 |
|
type(); |
| 118 |
|
set_field(); |
| 292 |
– |
generate_bonds(); |
| 119 |
|
} |
| 120 |
|
|
| 121 |
|
|
| 126 |
|
get_bonds(); |
| 127 |
|
get_angles(); |
| 128 |
|
get_torsions(); |
| 303 |
– |
get_coordbonds(); |
| 304 |
– |
|
| 305 |
– |
if (high_coord.ncoord > 0) |
| 306 |
– |
pot.use_highcoord = TRUE; |
| 129 |
|
|
| 130 |
|
attach(); |
| 309 |
– |
|
| 310 |
– |
|
| 131 |
|
get_rings(); |
| 132 |
|
// need allene |
| 133 |
|
|
| 134 |
|
// set active atoms |
| 135 |
|
set_active(); |
| 136 |
< |
|
| 136 |
> |
// setup non_bonded list of atoms to skip |
| 137 |
> |
for (i=1; i <= natom; i++) |
| 138 |
> |
{ |
| 139 |
> |
for (j=0; j < MAXIAT; j++) |
| 140 |
> |
if (atom[i].iat[j] != 0 && atom[i].bo[j] != 9) |
| 141 |
> |
{ |
| 142 |
> |
skip[i][atom[i].iat[j]] = i; |
| 143 |
> |
skip[atom[i].iat[j]][i] = atom[i].iat[j]; |
| 144 |
> |
} |
| 145 |
> |
for (j=0; j < attached.n13[i]; j++) |
| 146 |
> |
{ |
| 147 |
> |
skip[i][attached.i13[j][i]] = i; |
| 148 |
> |
skip[attached.i13[j][i]][i] = attached.i13[j][i]; |
| 149 |
> |
} |
| 150 |
> |
for(j=0; j < attached.n14[i]; j++) |
| 151 |
> |
{ |
| 152 |
> |
skip[i][attached.i14[j][i]] = -i; |
| 153 |
> |
skip[attached.i14[j][i]][i] = -attached.i14[j][i]; |
| 154 |
> |
} |
| 155 |
> |
} |
| 156 |
|
/* assign local geometry potential function parameters */ |
| 157 |
|
Missing_constants = FALSE; |
| 319 |
– |
// errfile = fopen_path(pcwindir,"pcmod.err","w"); |
| 158 |
|
if (pot.use_bond || pot.use_strbnd) nRet = kbond(); |
| 159 |
|
if (nRet == FALSE) // use end_calc to free memory |
| 160 |
|
{ |
| 323 |
– |
// message_alert("Parameters missing. See pcmod.err for information","Error"); |
| 324 |
– |
// fclose(errfile); |
| 161 |
|
energies.total = 9999.; |
| 162 |
|
return FALSE; |
| 163 |
|
} |
| 171 |
|
|
| 172 |
|
if (Missing_constants == TRUE) |
| 173 |
|
{ |
| 338 |
– |
// message_alert("Parameters missing. See pcmod.err for information","Error"); |
| 339 |
– |
// fclose(errfile); |
| 174 |
|
energies.total = 9999.0; |
| 175 |
|
return (FALSE); |
| 342 |
– |
} else |
| 343 |
– |
{ |
| 344 |
– |
// fclose(errfile); |
| 345 |
– |
// remove("pcmod.err"); |
| 176 |
|
} |
| 177 |
|
if (minim_values.iprint == TRUE) |
| 178 |
|
etot = print_energy(); |
| 208 |
|
energies.eurey = 0.0; |
| 209 |
|
energies.esolv = 0.0; |
| 210 |
|
energies.egeom =0.0; |
| 381 |
– |
|
| 382 |
– |
virial.virx = 0.0; |
| 383 |
– |
virial.viry = 0.0; |
| 384 |
– |
virial.virz = 0.0; |
| 211 |
|
|
| 212 |
|
for (i=1; i <= natom; i++) |
| 213 |
|
atom[i].energy = 0.0; |
| 265 |
|
{ |
| 266 |
|
double etot; |
| 267 |
|
int i; |
| 442 |
– |
// struct timeb start,end; |
| 268 |
|
|
| 269 |
|
energies.total = 0.0; |
| 270 |
|
energies.estr = 0.0; |
| 351 |
|
} |
| 352 |
|
|
| 353 |
|
/* ================================================================== */ |
| 529 |
– |
|
| 530 |
– |
int iscoord_bond(int i, int j) |
| 531 |
– |
{ |
| 532 |
– |
int k; |
| 533 |
– |
long int mask; |
| 534 |
– |
|
| 535 |
– |
mask = 1 << METCOORD_MASK ; |
| 536 |
– |
|
| 537 |
– |
for (k=0; k < MAXIAT; k++) |
| 538 |
– |
{ |
| 539 |
– |
if (atom[i].iat[k] == j && atom[i].bo[k] == 9) |
| 540 |
– |
{ |
| 541 |
– |
if (atom[i].type >= 300) |
| 542 |
– |
{ |
| 543 |
– |
if (atom[j].type == 2 || atom[j].type == 4 || atom[j].type == 29 || |
| 544 |
– |
atom[j].type == 30 || atom[j].type == 40 || atom[j].type == 48 ) |
| 545 |
– |
return TRUE; |
| 546 |
– |
} |
| 547 |
– |
if (atom[j].type >= 300) |
| 548 |
– |
{ |
| 549 |
– |
if (atom[i].type == 2 || atom[i].type == 4 || atom[i].type == 29 || |
| 550 |
– |
atom[i].type == 30 || atom[i].type == 40 || atom[i].type == 48 ) |
| 551 |
– |
return TRUE; |
| 552 |
– |
} |
| 553 |
– |
} |
| 554 |
– |
} |
| 555 |
– |
// throughout Metal-lone pairs if coordinated bond |
| 556 |
– |
// metal to donor atom |
| 557 |
– |
if ( (atom[i].type >= 300) && atom[j].flags & mask) |
| 558 |
– |
return TRUE; |
| 559 |
– |
if ( (atom[j].type >= 300) && atom[i].flags & mask) |
| 560 |
– |
return TRUE; |
| 561 |
– |
|
| 562 |
– |
return FALSE; |
| 563 |
– |
} |
| 564 |
– |
|
| 565 |
– |
void get_coordbonds() |
| 566 |
– |
{ |
| 567 |
– |
int i, j, k, iatype, jatm; |
| 568 |
– |
|
| 569 |
– |
cbonds.nbnd = 0; |
| 570 |
– |
pot.use_coordb = FALSE; |
| 571 |
– |
|
| 572 |
– |
for (i=1; i <= natom; i++) |
| 573 |
– |
{ |
| 574 |
– |
if (atom[i].mmx_type >= 300) |
| 575 |
– |
{ |
| 576 |
– |
for (j=0; j <= MAXIAT; j++) |
| 577 |
– |
{ |
| 578 |
– |
if (atom[i].bo[j] == 9) // coord bond |
| 579 |
– |
{ |
| 580 |
– |
iatype = atom[atom[i].iat[j]].mmx_type; |
| 581 |
– |
if (iatype == 2 || iatype == 4 || iatype == 29 || |
| 582 |
– |
iatype == 30 || iatype == 40 || iatype == 48 ) |
| 583 |
– |
{ |
| 584 |
– |
cbonds.icbonds[cbonds.nbnd][0] = i; |
| 585 |
– |
cbonds.icbonds[cbonds.nbnd][1] = atom[i].iat[j]; |
| 586 |
– |
cbonds.icbonds[cbonds.nbnd][2] = 0; |
| 587 |
– |
cbonds.nbnd++; |
| 588 |
– |
} else |
| 589 |
– |
{ |
| 590 |
– |
jatm = atom[i].iat[j]; |
| 591 |
– |
for (k = 0; k < MAXIAT; k++) |
| 592 |
– |
{ |
| 593 |
– |
if (atom[atom[jatm].iat[k]].mmx_type == 20) // lp |
| 594 |
– |
{ |
| 595 |
– |
cbonds.icbonds[cbonds.nbnd][0] = i; |
| 596 |
– |
cbonds.icbonds[cbonds.nbnd][1] = jatm; |
| 597 |
– |
cbonds.icbonds[cbonds.nbnd][2] = atom[jatm].iat[k]; |
| 598 |
– |
cbonds.nbnd++; |
| 599 |
– |
} |
| 600 |
– |
} |
| 601 |
– |
} |
| 602 |
– |
if (cbonds.nbnd > MAXCBND) |
| 603 |
– |
{ |
| 604 |
– |
fprintf(pcmlogfile,"Error - Too many coordinated bonds!\nProgram will now quit.\n"); |
| 605 |
– |
exit(0); |
| 606 |
– |
} |
| 607 |
– |
} |
| 608 |
– |
} |
| 609 |
– |
} |
| 610 |
– |
} |
| 611 |
– |
if (cbonds.nbnd > 0) |
| 612 |
– |
pot.use_coordb = TRUE; |
| 613 |
– |
} |
| 354 |
|
int isbond(int i, int j) |
| 355 |
|
{ |
| 356 |
|
int k; |
| 361 |
|
} |
| 362 |
|
return FALSE; |
| 363 |
|
} |
| 364 |
< |
|
| 364 |
> |
// ========================== |
| 365 |
|
void get_bonds() |
| 366 |
|
{ |
| 367 |
|
int i, j; |
| 628 |
– |
long int mask; |
| 368 |
|
|
| 369 |
< |
bonds_ff.nbnd = 0; |
| 631 |
< |
mask = 1L << 0; // flag for pi atoms |
| 632 |
< |
|
| 369 |
> |
bonds_ff.nbnd = 0; |
| 370 |
|
for (i=1; i <= natom; i++) |
| 371 |
|
{ |
| 372 |
|
for (j=i+1; j <= natom; j++) |
