| Rev. | 4 |
|---|---|
| Size | 11,024 bytes |
| Time | 2010-01-31 21:12:08 |
| Author | toshinagata1964 |
| Log Message | AmberTools-1.3 (part) is bundled.
|
Fork/* CHARMM */
int rcharmm(char *filename, int *atomnum, ATOM atom[], int *bondnum,
BOND bond[], CONTROLINFO *cinfo, MOLINFO *minfo)
{
int i;
int numatom;
int numatom2;
int numbond;
char tmpchar[MAXCHAR], tmpchar1[MAXCHAR], tmpchar2[MAXCHAR], tmpchar3[MAXCHAR], tmpchar4[MAXCHAR], tmpchar5[MAXCHAR];
char tmpchar6[MAXCHAR], tmpchar7[MAXCHAR], tmpchar8[MAXCHAR], tmpchar9[MAXCHAR], tmpchar10[MAXCHAR];
char line[MAXCHAR];
char rtf[MAXCHAR];
int irtf = 0;
int rflag = 0;
int flag1, flag2;
int bondi, bondj;
int overflow_flag = 0;
FILE *fpin;
if ((fpin = fopen(filename, "r")) == NULL) {
fprintf(stderr, "Cannot open the charmm input file: %s, exit\n", filename);
exit(1);
}
initial((*cinfo).maxatom, atom, (*minfo).resname);
strcpy(rtf, filename);
numatom = 0;
numbond = 0;
for (;;) {
if (fgets(line, MAXCHAR, fpin) == NULL) break;
if(line[0] == '*') continue;
strcpy(tmpchar1, "");
strcpy(tmpchar2, "");
strcpy(tmpchar3, "");
strcpy(tmpchar4, "");
strcpy(tmpchar5, "");
tmpchar1[0]='\0';
tmpchar2[0]='\0';
tmpchar3[0]='\0';
tmpchar4[0]='\0';
tmpchar5[0]='\0';
sscanf(line, "%s%s%s%s%s", tmpchar1, tmpchar2, tmpchar3, tmpchar4, tmpchar5);
if((irtf == 0) &&
(strcmp(tmpchar1, "Read") == 0 || strcmp(tmpchar1, "READ") == 0 || strcmp(tmpchar1, "read") == 0) &&
(strcmp(tmpchar2, "Rtf") == 0 || strcmp(tmpchar2, "RTF") == 0 || strcmp(tmpchar2, "rtf") == 0) &&
(strcmp(tmpchar3, "Card") == 0 || strcmp(tmpchar3, "CARD") == 0 || strcmp(tmpchar3, "card") == 0) &&
(strcmp(tmpchar4, "Name") == 0 || strcmp(tmpchar4, "NAME") == 0 || strcmp(tmpchar4, "name") == 0)) {
strcpy(rtf, tmpchar5);
irtf = 1;
continue;
}
if((rflag == 0) &&
(strcmp(tmpchar1, "Read") == 0 || strcmp(tmpchar1, "READ") == 0 || strcmp(tmpchar1, "read") == 0) &&
(strcmp(tmpchar2, "Coor") == 0 || strcmp(tmpchar2, "COOR") == 0 || strcmp(tmpchar2, "coor") == 0) &&
(strcmp(tmpchar3, "Card") == 0 || strcmp(tmpchar3, "CARD") == 0 || strcmp(tmpchar3, "card") == 0)) {
rflag = 1;
continue;
}
if(rflag == 1) {
sscanf(line, "%d", &numatom2);
if (numatom2 >= (*cinfo).maxatom && overflow_flag == 0) {
printf ("\nThe atom number exceeds the MAXATOM, reallocate memory");
overflow_flag = 1;
return overflow_flag;
}
rflag = 2;
numatom = 0;
continue;
}
if(rflag == 2) {
sscanf(line, "%d%s%s%s%lf%lf%lf", &atom[numatom].id, atom[numatom].resid, atom[numatom].aa, atom[numatom].name,
&atom[numatom].x, &atom[numatom].y, &atom[numatom].z);
numatom++;
if(numatom == numatom2) break;
}
}
fclose(fpin);
if ((fpin = fopen(rtf, "r")) == NULL) {
fprintf(stderr, "Cannot open the rtf file in rcharmm() : %s, exit\n", rtf);
exit(1);
}
numatom = 0;
numbond = 0;
for (;;) {
if (fgets(line, MAXCHAR, fpin) == NULL) break;
if(line[0] == '*') continue;
strcpy(tmpchar, "");
strcpy(tmpchar1, "");
strcpy(tmpchar2, "");
strcpy(tmpchar3, "");
strcpy(tmpchar4, "");
strcpy(tmpchar5, "");
strcpy(tmpchar6, "");
strcpy(tmpchar7, "");
strcpy(tmpchar8, "");
strcpy(tmpchar9, "");
strcpy(tmpchar10, "");
tmpchar[0]='\0';
tmpchar1[0]='\0';
tmpchar2[0]='\0';
tmpchar3[0]='\0';
tmpchar4[0]='\0';
tmpchar5[0]='\0';
tmpchar6[0]='\0';
tmpchar7[0]='\0';
tmpchar8[0]='\0';
tmpchar9[0]='\0';
tmpchar10[0]='\0';
sscanf(line, "%s%s%s%s%s%s%s%s%s%s%s", tmpchar, tmpchar1, tmpchar2, tmpchar3, tmpchar4, tmpchar5, tmpchar6,
tmpchar7, tmpchar8, tmpchar9, tmpchar10);
if(strcmp(tmpchar, "RESI") == 0)
(*minfo).dcharge = atof(tmpchar2);
if(strcmp(tmpchar, "ATOM") == 0) {
strcpy(atom[numatom].ambername, tmpchar2);
atom[numatom].charge = atof(tmpchar3);
numatom++;
}
if(strcmp(tmpchar, "BOND") == 0) {
if(strlen(tmpchar1) > 0 && strlen(tmpchar2) > 0) {
flag1 = 0;
flag2 = 0;
for(i=0;i<numatom2;i++) {
if(flag1 == 1 && flag2 == 1) break;
if(strcmp(tmpchar1, atom[i].name) == 0) {
bondi = i;
flag1 = 1;
}
if(strcmp(tmpchar2, atom[i].name) == 0) {
bondj = i;
flag2 = 1;
}
}
if(flag1 ==0 || flag2 == 0) continue;
if(overflow_flag == 0) {
bond[numbond].bondi = bondi;
bond[numbond].bondj = bondj;
}
numbond++;
if (numbond >= (*cinfo).maxbond && overflow_flag == 0) {
printf ("\nThe bond number exceeds the MAXBOND, reallocate memory");
overflow_flag = 1;
}
}
if(strlen(tmpchar3) > 0 && strlen(tmpchar4) > 0) {
flag1 = 0;
flag2 = 0;
for(i=0;i<numatom2;i++) {
if(flag1 == 1 && flag2 == 1) break;
if(strcmp(tmpchar3, atom[i].name) == 0) {
bondi = i;
flag1 = 1;
}
if(strcmp(tmpchar4, atom[i].name) == 0) {
bondj = i;
flag2 = 1;
}
}
if(flag1 ==0 || flag2 == 0) continue;
if(overflow_flag == 0) {
bond[numbond].bondi = bondi;
bond[numbond].bondj = bondj;
}
numbond++;
if (numbond >= (*cinfo).maxbond && overflow_flag == 0) {
printf ("\nThe bond number exceeds the MAXBOND, reallocate memory");
overflow_flag = 1;
}
}
if(strlen(tmpchar5) > 0 && strlen(tmpchar6) > 0) {
flag1 = 0;
flag2 = 0;
for(i=0;i<numatom2;i++) {
if(flag1 == 1 && flag2 == 1) break;
if(strcmp(tmpchar5, atom[i].name) == 0) {
bondi = i;
flag1 = 1;
}
if(strcmp(tmpchar6, atom[i].name) == 0) {
bondj = i;
flag2 = 1;
}
}
if(flag1 ==0 || flag2 == 0) continue;
if(overflow_flag == 0) {
bond[numbond].bondi = bondi;
bond[numbond].bondj = bondj;
}
numbond++;
if (numbond >= (*cinfo).maxbond && overflow_flag == 0) {
printf ("\nThe bond number exceeds the MAXBOND, reallocate memory");
overflow_flag = 1;
}
}
if(strlen(tmpchar7) > 0 && strlen(tmpchar8) > 0) {
flag1 = 0;
flag2 = 0;
for(i=0;i<numatom2;i++) {
if(flag1 == 1 && flag2 == 1) break;
if(strcmp(tmpchar7, atom[i].name) == 0) {
bondi = i;
flag1 = 1;
}
if(strcmp(tmpchar8, atom[i].name) == 0) {
bondj = i;
flag2 = 1;
}
}
if(flag1 ==0 || flag2 == 0) continue;
if(overflow_flag == 0) {
bond[numbond].bondi = bondi;
bond[numbond].bondj = bondj;
}
numbond++;
if (numbond >= (*cinfo).maxbond && overflow_flag == 0) {
printf ("\nThe bond number exceeds the MAXBOND, reallocate memory");
overflow_flag = 1;
}
}
if(strlen(tmpchar9) > 0 && strlen(tmpchar10) > 0) {
flag1 = 0;
flag2 = 0;
for(i=0;i<numatom2;i++) {
if(flag1 == 1 && flag2 == 1) break;
if(strcmp(tmpchar9, atom[i].name) == 0) {
bondi = i;
flag1 = 1;
}
if(strcmp(tmpchar10, atom[i].name) == 0) {
bondj = i;
flag2 = 1;
}
}
if(flag1 ==0 || flag2 == 0) continue;
if(overflow_flag == 0) {
bond[numbond].bondi = bondi;
bond[numbond].bondj = bondj;
}
numbond++;
if (numbond >= (*cinfo).maxbond && overflow_flag == 0) {
printf ("\nThe bond number exceeds the MAXBOND, reallocate memory");
overflow_flag = 1;
}
}
}
}
*bondnum = numbond;
*atomnum = numatom2;
return overflow_flag;
}
/* CHARMM */
void wcharmm(char *filename, char *ifilename, int atomnum, ATOM * atom,
int bondnum, BOND * bond, CONTROLINFO cinfo, MOLINFO minfo)
{
char tmpchar[MAXCHAR];
size_t copied_size;
wac("ANTECHAMBER_PREP.AC0", atomnum, atom, bondnum, bond, cinfo,
minfo);
system("cp -rf ANTECHAMBER_PREP.AC0 ANTECHAMBER_PREP.AC");
/*part1: if intype is not prepi, prepc and ac, judge atom type*/
if ((strcmp(cinfo.intype, "prepi") != 0 &&
strcmp(cinfo.intype, "prepc") != 0 &&
strcmp(cinfo.intype, "5") != 0 &&
strcmp(cinfo.intype, "6") != 0 &&
strcmp(cinfo.intype, "ac") != 0 &&
strcmp(cinfo.intype, "1") != 0) || cinfo.prediction_index == 1
|| cinfo.prediction_index == 3) {
copied_size = build_exe_path(tmpchar, "atomtype"
" -i ANTECHAMBER_PREP.AC0 -o ANTECHAMBER_PREP.AC -p "
, MAXCHAR );
strncat(tmpchar, minfo.atom_type_def, MAXCHAR - copied_size );
if(cinfo.intstatus == 2)
fprintf(stderr, "\nRunning: %s\n", tmpchar);
system(tmpchar);
}
copied_size = build_exe_path(tmpchar, "charmmgen"
" -i ANTECHAMBER_PREP.AC -f ac -o "
, MAXCHAR );
strncat(tmpchar, filename, MAXCHAR - copied_size );
strcat(tmpchar, " -r ");
strcat(tmpchar, minfo.resname);
if(cinfo.intstatus == 2)
fprintf(stderr, "\nRunning: %s\n", tmpchar);
system(tmpchar);
/* system("rm -f ANTECHAMBER_PREP.AC");*/
}