Sat Oct 15 14:21:13 PDT 2011 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph2.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb2.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sat Oct 15 2011 at 14:21:13 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 347 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4769 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5117589 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): -15.98600 37.20100 ymin,ymax (A): -30.94100 34.00100 zmin,zma (A): -3.900000 65.66400 x,y,z range (A): 53.18700 64.94200 69.56400 scale (grids/A): 0.5117589 object centre (A): 10.60750 1.530002 30.88200 number of atom coordinates read : 4769 total number of charged atoms : 4518 net assigned charge : 8.706045 assigned positive charge : 717.0836 centred at (gu) : 89.65780 90.67527 88.37147 assigned negative charge : -708.3820 centred at (gu) : 89.56052 90.76560 88.33487 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 7932 nv = 96 ne = 84 npr = 95598 no. pairs analyzed = 95598 no. exposed pairs = 6117 no. arc points = 42507 no. surface atoms = 2048 nbur = 2721 mkacc time = 0.2500000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.680000 m= 295 mr = 4043 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5100000 number of dielectric boundary points 4181 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4048 ## 596 charges are in solution ## iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 10525 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.1181167E-11 1.5276713E-10 midg,1,midg; midg,igrid,midg 3.1404404E-10 -1.3508229E-10 1,midg,midg; igrid,midg,midg -1.4397818E-10 3.5926964E-10 gauss-seidel spectral radius is 0.9804756 estimated iterations to convergence 59 setup time was (sec) 0.8800000 now iterating at: 14:21:14 rms-change max change #iterations 6.9868214E-02 11.74273 at 10iterations 4.0524546E-03 0.5838337 at 20iterations 4.4570552E-04 6.1978936E-02 at 30iterations 1.5487178E-04 2.4234533E-02 at 40iterations 6.2487430E-05 9.9768639E-03 at 50iterations finished qdiffx linear iterations at : 14:21:19 total time elapsed so far: 5.640000 # loops : 50 mean,max change (kT/e) : 6.2487430E-05 9.9768639E-03 energy calculations done at 5.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.810000 DelPhi exited at 14:21:20 5.811u 0.443s 0:06.64 94.1% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sat Oct 15 2011 at 14:21:20 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 347 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4769 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.535277 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): -15.98600 37.20100 ymin,ymax (A): -30.94100 34.00100 zmin,zma (A): -3.900000 65.66400 x,y,z range (A): 53.18700 64.94200 69.56400 scale (grids/A): 1.535277 object centre (A): 10.60750 1.530002 30.88200 number of atom coordinates read : 4769 total number of charged atoms : 4518 net assigned charge : 8.706045 assigned positive charge : 717.0836 centred at (gu) : 88.97230 92.02415 85.11277 assigned negative charge : -708.3820 centred at (gu) : 88.68105 92.29650 85.00435 start vw surface at 0.1700000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 90697 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42507 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 26331 mr = 62181 m= 2263 mr = 17267 m= 47 mr = 978 m= 0 mr = 10 time to grow re-entrant surface = 0.4100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7800000 number of dielectric boundary points 38902 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 558 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.9100000 number of grid points assigned charge 34049 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.5117589 object centre at (A) : 10.60750 1.530002 30.88200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.8905907E-03 2.2608511E-02 midg,1,midg; midg,igrid,midg 1.1623364E-02 -1.4228283E-02 1,midg,midg; igrid,midg,midg -8.7978246E-05 9.9919345E-03 gauss-seidel spectral radius is 0.9981264 estimated iterations to convergence 184 setup time was (sec) 1.140000 now iterating at: 14:21:21 rms-change max change #iterations 3.796711 148.6758 at 10iterations 1.558899 52.61918 at 20iterations 0.6424162 23.39162 at 30iterations 0.2652710 8.591391 at 40iterations 0.1087525 3.671166 at 50iterations 4.5006223E-02 1.443926 at 60iterations 1.8530076E-02 0.6501303 at 70iterations 7.6636570E-03 0.2544198 at 80iterations 3.1785434E-03 9.9013090E-02 at 90iterations 1.3293077E-03 4.3174744E-02 at 100iterations 5.7401281E-04 1.9229889E-02 at 110iterations 2.6807832E-04 9.4804764E-03 at 120iterations finished qdiffx linear iterations at : 14:21:34 total time elapsed so far: 13.37000 # loops : 120 mean,max change (kT/e) : 2.6807832E-04 9.4804764E-03 energy calculations done at 13.37000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.54000 DelPhi exited at 14:21:34 13.540u 0.533s 0:14.38 97.8% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sat Oct 15 2011 at 14:21:34 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 347 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4769 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.302915 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): -15.98600 37.20100 ymin,ymax (A): -30.94100 34.00100 zmin,zma (A): -3.900000 65.66400 x,y,z range (A): 53.18700 64.94200 69.56400 scale (grids/A): 2.302915 object centre (A): 10.60750 1.530002 30.88200 number of atom coordinates read : 4769 total number of charged atoms : 4518 net assigned charge : 8.706045 assigned positive charge : 717.0836 centred at (gu) : 88.45827 93.03615 82.66875 assigned negative charge : -708.3820 centred at (gu) : 88.02164 93.44481 82.50638 start vw surface at 0.1800000 fill in re-entrant regions at 0.5800000 boundary points on vw surface= 211790 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42507 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 94313 mr = 153217 m= 23612 mr = 73479 m= 3213 mr = 16648 m= 166 mr = 1979 m= 1 mr = 59 m= 0 mr = 0 time to grow re-entrant surface = 1.180000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.910000 number of dielectric boundary points 87713 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 61 iepsmp to db, and charging done at 2.070000 number of grid points assigned charge 36046 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 1.535277 object centre at (A) : 10.60750 1.530002 30.88200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1492800 0.5352951 midg,1,midg; midg,igrid,midg 0.1555853 -0.2945219 1,midg,midg; igrid,midg,midg -3.1347030E-03 0.1433243 gauss-seidel spectral radius is 0.9991688 estimated iterations to convergence 274 setup time was (sec) 2.310000 now iterating at: 14:21:37 rms-change max change #iterations 10.27298 278.4278 at 10iterations 5.896925 148.6903 at 20iterations 3.358476 81.09199 at 30iterations 1.901542 48.03764 at 40iterations 1.074139 24.79725 at 50iterations 0.6043552 13.94703 at 60iterations 0.3398608 7.344948 at 70iterations 0.1905329 3.682899 at 80iterations 0.1068168 2.328434 at 90iterations 5.9681661E-02 1.196241 at 100iterations 3.3275712E-02 0.6236086 at 110iterations 1.8558810E-02 0.3929539 at 120iterations 1.0379314E-02 0.1895866 at 130iterations 5.7867798E-03 0.1200312 at 140iterations 3.2186084E-03 6.5547943E-02 at 150iterations 1.7971982E-03 3.6277771E-02 at 160iterations 1.0022840E-03 1.9186974E-02 at 170iterations 5.6112185E-04 1.2268066E-02 at 180iterations finished qdiffx linear iterations at : 14:21:57 total time elapsed so far: 22.51000 # loops : 180 mean,max change (kT/e) : 5.6112185E-04 1.2268066E-02 energy calculations done at 22.51000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 22.69000 DelPhi exited at 14:21:58 22.695u 0.567s 0:23.56 98.6% 0+0k 0+0io 0pf+0w