Mon Oct 10 17:01:46 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 Mon Oct 10 2011 at 17:01:46 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: 343 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2976 !!! WARNING: HIT 107 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6050614 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): -8.372000 48.59100 ymin,ymax (A): -8.696000 38.64000 zmin,zma (A): -3.478000 55.35900 x,y,z range (A): 56.96301 47.33600 58.83700 scale (grids/A): 0.6050614 object centre (A): 20.10950 14.97200 25.94050 number of atom coordinates read : 2976 total number of charged atoms : 2834 net assigned charge : -3.985963 assigned positive charge : 451.3799 centred at (gu) : 89.17686 89.63692 89.24450 assigned negative charge : -455.3671 centred at (gu) : 89.06784 89.53282 89.12988 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7277 nv = 96 ne = 84 npr = 60022 no. pairs analyzed = 60022 no. exposed pairs = 3831 no. arc points = 26957 no. surface atoms = 1300 nbur = 1676 mkacc time = 9.9999994E-02 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 = 1.456000 m= 318 mr = 3824 m= 0 mr = 29 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 47 time to turn everything in is 0.2000000 number of dielectric boundary points 3742 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2725 ## 273 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 9084 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.1207157E-09 3.1583578E-09 midg,1,midg; midg,igrid,midg -7.7536439E-09 2.9904219E-09 1,midg,midg; igrid,midg,midg -8.9160528E-09 2.8828790E-09 gauss-seidel spectral radius is 0.9858969 estimated iterations to convergence 69 setup time was (sec) 0.3900000 now iterating at: 17:01:47 rms-change max change #iterations 0.1209863 19.77058 at 10iterations 1.0706364E-02 1.474141 at 20iterations 9.3062251E-04 0.1597385 at 30iterations 7.9801968E-05 1.2123108E-02 at 40iterations 6.9237622E-06 9.9086761E-04 at 50iterations finished qdiffx linear iterations at : 17:01:50 total time elapsed so far: 3.230000 # loops : 50 mean,max change (kT/e) : 6.9237622E-06 9.9086761E-04 energy calculations done at 3.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.360000 DelPhi exited at 17:01:52 3.364u 0.192s 0:05.72 62.0% 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 Mon Oct 10 2011 at 17:01:53 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: 343 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2976 !!! WARNING: HIT 107 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.815184 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): -8.372000 48.59100 ymin,ymax (A): -8.696000 38.64000 zmin,zma (A): -3.478000 55.35900 x,y,z range (A): 56.96301 47.33600 58.83700 scale (grids/A): 1.815184 object centre (A): 20.10950 14.97200 25.94050 number of atom coordinates read : 2976 total number of charged atoms : 2834 net assigned charge : -3.985963 assigned positive charge : 451.3799 centred at (gu) : 87.52953 88.90966 87.73264 assigned negative charge : -455.3671 centred at (gu) : 87.20306 88.59800 87.38934 start vw surface at 0.1000000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 79502 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26957 grid for indexing accessible points = 1.400000 m= 26206 mr = 54268 m= 3275 mr = 18397 m= 112 mr = 1823 m= 2 mr = 22 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 1284 time to turn everything in is 0.3800000 number of dielectric boundary points 34587 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 196 iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 22159 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) : 0.6050614 object centre at (A) : 20.10950 14.97200 25.94050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.6674849E-03 2.4129976E-02 midg,1,midg; midg,igrid,midg -2.0639209E-02 7.7333036E-03 1,midg,midg; igrid,midg,midg -4.4517573E-02 2.2940367E-02 gauss-seidel spectral radius is 0.9985392 estimated iterations to convergence 207 setup time was (sec) 0.5900000 now iterating at: 17:01:53 rms-change max change #iterations 4.241042 187.4214 at 10iterations 1.927725 63.09006 at 20iterations 0.8741593 32.97335 at 30iterations 0.3989689 12.22565 at 40iterations 0.1814088 5.608006 at 50iterations 8.2739279E-02 2.708710 at 60iterations 3.7609980E-02 1.124786 at 70iterations 1.7228302E-02 0.5466311 at 80iterations 7.8428136E-03 0.2572594 at 90iterations 3.5816878E-03 0.1179900 at 100iterations 1.6329932E-03 4.9364090E-02 at 110iterations 7.4369524E-04 2.2066116E-02 at 120iterations finished qdiffx linear iterations at : 17:02:00 total time elapsed so far: 7.640000 # loops : 120 mean,max change (kT/e) : 7.4369524E-04 2.2066116E-02 energy calculations done at 7.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.780000 DelPhi exited at 17:02:02 7.781u 0.195s 0:09.16 87.0% 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 Mon Oct 10 2011 at 17:02:02 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: 343 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2976 !!! WARNING: HIT 107 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.722776 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): -8.372000 48.59100 ymin,ymax (A): -8.696000 38.64000 zmin,zma (A): -3.478000 55.35900 x,y,z range (A): 56.96301 47.33600 58.83700 scale (grids/A): 2.722776 object centre (A): 20.10950 14.97200 25.94050 number of atom coordinates read : 2976 total number of charged atoms : 2834 net assigned charge : -3.985963 assigned positive charge : 451.3799 centred at (gu) : 86.29404 88.36433 86.59875 assigned negative charge : -455.3671 centred at (gu) : 85.80447 87.89689 86.08402 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 184336 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26957 grid for indexing accessible points = 1.400000 m= 87611 mr = 132245 m= 27970 mr = 70164 m= 5449 mr = 21435 m= 537 mr = 3875 m= 18 mr = 292 m= 0 mr = 3 time to grow re-entrant surface = 0.5500000 no. cavity mid-points inaccessible to solvent = 4241 time to turn everything in is 0.9700000 number of dielectric boundary points 77907 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.060000 number of grid points assigned charge 22670 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) : 1.815184 object centre at (A) : 20.10950 14.97200 25.94050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1360763 0.4064221 midg,1,midg; midg,igrid,midg -0.1999967 0.1131438 1,midg,midg; igrid,midg,midg -0.5112854 0.4028889 gauss-seidel spectral radius is 0.9992483 estimated iterations to convergence 288 setup time was (sec) 1.210000 now iterating at: 17:02:04 rms-change max change #iterations 10.34432 328.7159 at 10iterations 6.062726 147.8066 at 20iterations 3.527477 96.45856 at 30iterations 2.039095 41.94072 at 40iterations 1.176613 23.86930 at 50iterations 0.6802382 14.62131 at 60iterations 0.3903536 8.337935 at 70iterations 0.2240443 4.172962 at 80iterations 0.1282960 2.503265 at 90iterations 7.3647067E-02 1.446848 at 100iterations 4.2198952E-02 0.8099976 at 110iterations 2.4214922E-02 0.4372387 at 120iterations 1.3843328E-02 0.2389393 at 130iterations 7.9240529E-03 0.1436033 at 140iterations 4.5362664E-03 7.9091072E-02 at 150iterations 2.5962177E-03 5.2399635E-02 at 160iterations 1.4858675E-03 2.7070045E-02 at 170iterations 8.5228746E-04 1.4698029E-02 at 180iterations finished qdiffx linear iterations at : 17:02:15 total time elapsed so far: 12.55000 # loops : 180 mean,max change (kT/e) : 8.5228746E-04 1.4698029E-02 energy calculations done at 12.55000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.67000 DelPhi exited at 17:02:15 12.675u 0.216s 0:13.46 95.6% 0+0k 0+0io 0pf+0w