コード例 #1
0
void SaveOptPdb(char szName[])
{
	int i;
	for(i=0; i<n_Phi; i++)	{
		Mol.QueryDihedral(IdxDihSelect[i]);
		Mol.Edit_Dihedral(IdxDihSelect[i], Phi_To_Set_Scan[i]);
	}
	Mol.SavePdb(szName);
}
コード例 #2
0
void MM_Fixed_1D_Scan(void)
{
	int i, Phi, Count;

	RestoreCoordinates();
	for(i=0; i<n_Phi; i++)	{
		Mol.QueryDihedral(IdxDihSelect[i]);
		Mol.Edit_Dihedral(IdxDihSelect[i], Phi_To_Set[i]);
	}
	
	Count = 0;
	for(Phi=-180; Phi<=180; Phi+=BIN_SIZE)	{	// 1D scan for this rotamer
		Phi_To_Set[Active_Phi] = Phi*1.0;
		Mol.QueryDihedral(IdxDihSelect[Active_Phi]);
		Mol.Edit_Dihedral(IdxDihSelect[Active_Phi], Phi_To_Set[Active_Phi]);
		E_Phi[Count] = Mol.Cal_E(0);
		Count++;
	}

	return;
}
コード例 #3
0
void Output_Gaussian_File(void)
{
	FILE *fOut, *fIn;
	int i, nAtom, IdxScan;
	char szNameGjf[256], szCmd[256], szName_Output[256];

	Determine_QM_Scan_Part();

	nAtom = Mol.nAtom;
	for(IdxScan=0; IdxScan<n_QM_Part; IdxScan++)	{
		Mol.QueryDihedral(IdxDihSelect[Active_Phi]);
		Mol.Edit_Dihedral(IdxDihSelect[Active_Phi], Phi_QM_Start[IdxScan]);

		sprintf(szNameGjf, "qm-scan-%d-%d.gjf", Active_Phi+1, IdxScan+1);
		fOut = fopen(szNameGjf, "w");
		fprintf(fOut, "%s", szQM_Level_1D_Scan_Cmd);
		for(i=0; i<nAtom; i++)	{
//			fprintf(fOut, "%c  %9.5lf %9.5lf %9.5lf\n", Mol.AtomName[i][0], Mol.x[i], Mol.y[i], Mol.z[i]);
			fprintf(fOut, "%s  %9.5lf %9.5lf %9.5lf\n", szElemName[i], Mol.x[i], Mol.y[i], Mol.z[i]);
		}
		fprintf(fOut, "\n");
		
		for(i=0; i<n_Phi; i++)	{
			if(i == Active_Phi)	{
				fprintf(fOut, "%s", szQM_Scan[IdxScan]);
			}
			else	{
				fprintf(fOut, "%d %d %d %d F\n", DihList[i][0]+1, DihList[i][1]+1, DihList[i][2]+1, DihList[i][3]+1);
			}
		}
		fprintf(fOut, "\n");
		fclose(fOut);

		sprintf(szName_Output, "qm-1d-phi-%d-p%d.out", Active_Phi+1, IdxScan+1);
		sprintf(szCmd, "%s < %s > %s", szExe_G09, szNameGjf, szName_Output);


		fIn = fopen(szName_Output, "r");
		if(fIn == NULL)	{
			system(szCmd);
		}
		else	{
			fclose(fIn);
		}

		Extract_Coord_E(szName_Output, Active_Phi, IdxScan);
	}
}
コード例 #4
0
int main(int argc, char **argv)
{
	int i;
	FILE *fOut;
	char szName[256];


	fFile_Run_Log = fopen("qm-1d-scan.log", "w");

//	MPI_Init(&argc, &argv);
//	MPI_Comm_rank(MPI_COMM_WORLD, &ProgID);
//	MPI_Comm_size(MPI_COMM_WORLD, &nProc);

	Get_EXE_Path("G09_EXE_PATH", szExe_G09);

	n_Bins = 360/BIN_SIZE+1;


	ForceField.ReadForceField(szForceFiled);
	Mol.ReadPSF(szXpsfFile, 0);
	Get_Netcharge_From_Xpsf();
	Setup_QM_Level();
	ReadElementList();

	Mol.AssignForceFieldParameters(&ForceField);
	Mol.ReadCRD(szCrdFile);
	BackupCoordinates();

	Read_Soft_DihedralList();

	for(Active_Phi=0; Active_Phi<n_Phi; Active_Phi++)	{
		RestoreCoordinates();
		for(i=0; i<n_Phi; i++)	{
			Phi_To_Set[i] = Mol.QueryDihedral(IdxDihSelect[i]);
			Mol.Edit_Dihedral(IdxDihSelect[i], Phi_To_Set[i]);
		}

		MM_Fixed_1D_Scan();
		E_Barrier_Lowest = Get_Barrier(E_Phi, n_Bins, E_Min, Phi_Save);
		E_Min_Save = E_Min;
		E_Min_Org = E_Min + E_RANGE;
		memcpy(E_Scan, E_Phi, sizeof(double)*n_Bins);
		memcpy(Phi_To_Set_Scan, Phi_To_Set, sizeof(double)*n_Phi);
		Phi_To_Set_Scan[Active_Phi] = Phi_Save;

		sprintf(szName, "ini-%d.dat", Active_Phi+1);
		fOut = fopen(szName, "w");
		for(i=0; i<n_Bins; i++)	{
			fprintf(fOut, "%5d %8.5E\n", -180+i*BIN_SIZE, E_Scan[i]-E_Min);
		}
		fclose(fOut);

		sprintf(szName, "ini-%d.pdb", Active_Phi+1);
		SaveOptPdb(szName);

		n_State_List[Active_Phi] = 1;
		Enumerate_Dihedrals(0);
		n_State_List[Active_Phi] = n_State_List_Save[Active_Phi];

		sprintf(szName, "end-%d.dat", Active_Phi+1);
		fOut = fopen(szName, "w");
		for(i=0; i<n_Bins; i++)	{
			fprintf(fOut, "%5d %8.5E\n", -180+i*BIN_SIZE, E_Scan[i]-E_Min_Save);
		}
		fclose(fOut);

		sprintf(szName, "end-%d.pdb", Active_Phi+1);
		SaveOptPdb(szName);

		sprintf(szName, "phi-%d.dat", Active_Phi+1);
		fOut = fopen(szName, "w");
		for(i=0; i<n_Phi; i++)	{
			fprintf(fOut, "%lf\n", Phi_To_Set_Scan[i]);
		}
		fclose(fOut);

	
		Output_Gaussian_File();
	}


	Reorganize_QM_1D_Scan_Data();

	fclose(fFile_Run_Log);

//	MPI_Barrier(MPI_COMM_WORLD);
//	MPI_Finalize();

	return 0;
}
コード例 #5
0
int main(int argc, char **argv)
{
	int i;
	FILE *fOut;
	char szName[256], *szEnv;

//	SetEnvironmentVariable(szGAUSS_SCRDIR, "c:\\1");

	fFile_Run_Log = fopen("qm-1d-scan.log", "w");
	
	szEnv = getenv(szGAUSS_SCRDIR);
	if (szEnv == NULL) {
		Quit_With_Error_Msg("Environment variable $GAUSS_SCRDIR is NOT set.\nQuit\n");
	}
	strcpy(szGAUSS_SCRDIR_Base, szEnv);
	


	Get_EXE_Path("G09_EXE_PATH", szExe_G09);

	n_Bins = 360/BIN_SIZE+1;


	ForceField.ReadForceField(szForceFiled);
	Mol.ReadPSF(szXpsfFile, 0);
	Get_Netcharge_From_Xpsf();
	Setup_QM_Level();
	ReadElementList();

	Mol.AssignForceFieldParameters(&ForceField);
	Mol.ReadCRD(szCrdFile);
	BackupCoordinates();

	Read_Soft_DihedralList();

	nJob = nJobDone = 0;

	for(Active_Phi=0; Active_Phi<n_Phi; Active_Phi++)	{
		RestoreCoordinates();
		for(i=0; i<n_Phi; i++)	{
			Phi_To_Set[i] = Mol.QueryDihedral(IdxDihSelect[i]);
			Mol.Edit_Dihedral(IdxDihSelect[i], Phi_To_Set[i]);
		}

		MM_Fixed_1D_Scan();
		E_Barrier_Lowest = Get_Barrier(E_Phi, n_Bins, E_Min, Phi_Save);
		E_Min_Save = E_Min;
		E_Min_Org = E_Min + E_RANGE;
		memcpy(E_Scan, E_Phi, sizeof(double)*n_Bins);
		memcpy(Phi_To_Set_Scan, Phi_To_Set, sizeof(double)*n_Phi);
		Phi_To_Set_Scan[Active_Phi] = Phi_Save;

		sprintf(szName, "ini-%d.dat", Active_Phi+1);
		fOut = fopen(szName, "w");
		for(i=0; i<n_Bins; i++)	{
			fprintf(fOut, "%5d %8.5E\n", -180+i*BIN_SIZE, E_Scan[i]-E_Min);
		}
		fclose(fOut);

		sprintf(szName, "ini-%d.pdb", Active_Phi+1);
		SaveOptPdb(szName);

		n_State_List[Active_Phi] = 1;
		Enumerate_Dihedrals(0);
		n_State_List[Active_Phi] = n_State_List_Save[Active_Phi];

		sprintf(szName, "end-%d.dat", Active_Phi+1);
		fOut = fopen(szName, "w");
		for(i=0; i<n_Bins; i++)	{
			fprintf(fOut, "%5d %8.5E\n", -180+i*BIN_SIZE, E_Scan[i]-E_Min_Save);
		}
		fclose(fOut);

		sprintf(szName, "end-%d.pdb", Active_Phi+1);
		SaveOptPdb(szName);

		sprintf(szName, "phi-%d.dat", Active_Phi+1);
		fOut = fopen(szName, "w");
		for(i=0; i<n_Phi; i++)	{
			fprintf(fOut, "%lf\n", Phi_To_Set_Scan[i]);
		}
		fclose(fOut);

	
		Output_Gaussian_File();
	}

	if(nJob > 0)	{
		RunAllJobs();
		Exatract_All_Info_QM_1D_Scan();
		Reorganize_QM_1D_Scan_Data();
	}

	fclose(fFile_Run_Log);

	return 0;
}