Sun Oct 9 08:09:12 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+sph.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 = amb.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 Sun Oct 9 2011 at 08:09:12 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2253 !!! WARNING: NAP 276 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6609729 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): 28.67800 82.53800 ymin,ymax (A): 77.71000 128.8460 zmin,zma (A): 27.86000 74.82000 x,y,z range (A): 53.86000 51.13599 46.96000 scale (grids/A): 0.6609729 object centre (A): 55.60800 103.2780 51.34000 number of atom coordinates read : 2253 total number of charged atoms : 2120 net assigned charge : 3.500021 assigned positive charge : 333.0370 centred at (gu) : 88.51570 92.14677 88.69772 assigned negative charge : -329.5372 centred at (gu) : 88.48719 92.13866 88.75304 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6751 nv = 96 ne = 84 npr = 45939 no. pairs analyzed = 45939 no. exposed pairs = 2747 no. arc points = 19374 no. surface atoms = 926 nbur = 1327 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 388 mr = 3807 m= 1 mr = 52 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1700000 number of dielectric boundary points 3281 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1849 ## 157 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 7842 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.4054899E-08 -2.9823441E-10 midg,1,midg; midg,igrid,midg 4.9815871E-09 1.6044948E-08 1,midg,midg; igrid,midg,midg 5.3911102E-09 1.0229319E-08 gauss-seidel spectral radius is 0.9881091 estimated iterations to convergence 75 setup time was (sec) 0.3700000 now iterating at: 08:09:12 rms-change max change #iterations 0.1582314 28.25829 at 10iterations 1.6733089E-02 2.420761 at 20iterations 1.8170289E-03 0.2885160 at 30iterations 1.9076891E-04 2.8343201E-02 at 40iterations 2.0600510E-05 2.8362274E-03 at 50iterations finished qdiffx linear iterations at : 08:09:15 total time elapsed so far: 3.240000 # loops : 50 mean,max change (kT/e) : 2.0600510E-05 2.8362274E-03 energy calculations done at 3.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.370000 DelPhi exited at 08:09:16 3.369u 0.180s 0:03.83 92.4% 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 Sun Oct 9 2011 at 08:09:16 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2253 !!! WARNING: NAP 276 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.982919 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): 28.67800 82.53800 ymin,ymax (A): 77.71000 128.8460 zmin,zma (A): 27.86000 74.82000 x,y,z range (A): 53.86000 51.13599 46.96000 scale (grids/A): 1.982919 object centre (A): 55.60800 103.2780 51.34000 number of atom coordinates read : 2253 total number of charged atoms : 2120 net assigned charge : 3.500021 assigned positive charge : 333.0370 centred at (gu) : 85.54716 96.44013 86.09316 assigned negative charge : -329.5372 centred at (gu) : 85.46162 96.41624 86.25918 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 73306 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19374 grid for indexing accessible points = 1.400000 m= 26534 mr = 51554 m= 4429 mr = 19845 m= 343 mr = 2797 m= 7 mr = 152 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 2340 time to turn everything in is 0.3500000 number of dielectric boundary points 30271 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 86 iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 16748 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) : 0.6609729 object centre at (A) : 55.60800 103.2780 51.34000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0835124E-02 1.2732042E-03 midg,1,midg; midg,igrid,midg 7.2128521E-03 -3.5938449E-04 1,midg,midg; igrid,midg,midg 9.4643226E-03 2.0058859E-02 gauss-seidel spectral radius is 0.9987036 estimated iterations to convergence 220 setup time was (sec) 0.5600000 now iterating at: 08:09:17 rms-change max change #iterations 4.212490 198.4686 at 10iterations 2.003268 71.28220 at 20iterations 0.9589568 33.49792 at 30iterations 0.4566734 13.79691 at 40iterations 0.2181046 6.720985 at 50iterations 0.1041762 3.272705 at 60iterations 4.9792618E-02 1.652802 at 70iterations 2.3812018E-02 0.7275906 at 80iterations 1.1351801E-02 0.3836420 at 90iterations 5.4235011E-03 0.1864166 at 100iterations 2.6005986E-03 8.4583282E-02 at 110iterations 1.2406876E-03 3.6889076E-02 at 120iterations finished qdiffx linear iterations at : 08:09:24 total time elapsed so far: 7.650000 # loops : 120 mean,max change (kT/e) : 1.2406876E-03 3.6889076E-02 energy calculations done at 7.650000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.790000 DelPhi exited at 08:09:24 7.789u 0.213s 0:08.28 96.4% 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 Sun Oct 9 2011 at 08:09:24 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2253 !!! WARNING: NAP 276 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.974378 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): 28.67800 82.53800 ymin,ymax (A): 77.71000 128.8460 zmin,zma (A): 27.86000 74.82000 x,y,z range (A): 53.86000 51.13599 46.96000 scale (grids/A): 2.974378 object centre (A): 55.60800 103.2780 51.34000 number of atom coordinates read : 2253 total number of charged atoms : 2120 net assigned charge : 3.500021 assigned positive charge : 333.0370 centred at (gu) : 83.32072 99.66031 84.13971 assigned negative charge : -329.5372 centred at (gu) : 83.19243 99.62442 84.38889 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 169533 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19374 grid for indexing accessible points = 1.400000 m= 85236 mr = 124518 m= 31842 mr = 70257 m= 8142 mr = 26048 m= 1375 mr = 6179 m= 144 mr = 947 m= 2 mr = 68 m= 0 mr = 0 time to grow re-entrant surface = 0.5200000 no. cavity mid-points inaccessible to solvent = 7927 time to turn everything in is 0.9200000 number of dielectric boundary points 68257 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.010000 number of grid points assigned charge 16960 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) : 1.982919 object centre at (A) : 55.60800 103.2780 51.34000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.8958355E-03 1.9185239E-02 midg,1,midg; midg,igrid,midg 6.0895126E-02 -0.1688658 1,midg,midg; igrid,midg,midg -3.6330219E-02 0.3006163 gauss-seidel spectral radius is 0.9992695 estimated iterations to convergence 292 setup time was (sec) 1.160000 now iterating at: 08:09:25 rms-change max change #iterations 9.741303 341.4868 at 10iterations 5.712389 144.8374 at 20iterations 3.351221 81.03133 at 30iterations 1.949594 37.09484 at 40iterations 1.132898 27.11927 at 50iterations 0.6572202 12.91115 at 60iterations 0.3814418 6.796066 at 70iterations 0.2199537 3.964176 at 80iterations 0.1272781 2.376734 at 90iterations 7.3501408E-02 1.370005 at 100iterations 4.2441119E-02 0.7595234 at 110iterations 2.4482863E-02 0.4398913 at 120iterations 1.4142299E-02 0.2451935 at 130iterations 8.1551895E-03 0.1488209 at 140iterations 4.7066435E-03 8.5037231E-02 at 150iterations 2.7165324E-03 4.9072266E-02 at 160iterations 1.5629737E-03 2.6848793E-02 at 170iterations 9.0113305E-04 1.5622616E-02 at 180iterations finished qdiffx linear iterations at : 08:09:37 total time elapsed so far: 12.29000 # loops : 180 mean,max change (kT/e) : 9.0113305E-04 1.5622616E-02 energy calculations done at 12.29000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.42000 DelPhi exited at 08:09:37 12.421u 0.201s 0:12.89 97.9% 0+0k 0+0io 0pf+0w