Sun Oct 9 08:00:19 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 Sun Oct 9 2011 at 08:00:19 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: 325 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2204 !!! WARNING: NDP 385 has a net charge of -3.0000 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: 0.6929710 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): 4.386000 50.00300 ymin,ymax (A): -25.23700 26.13600 zmin,zma (A): -19.74500 30.20500 x,y,z range (A): 45.61700 51.37300 49.95000 scale (grids/A): 0.6929710 object centre (A): 27.19450 0.4495001 5.230000 number of atom coordinates read : 2204 total number of charged atoms : 2062 net assigned charge : -3.499990 assigned positive charge : 336.9805 centred at (gu) : 90.10527 91.01839 90.11209 assigned negative charge : -340.4807 centred at (gu) : 90.12507 91.09847 90.20202 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 7336 nv = 96 ne = 84 npr = 44211 no. pairs analyzed = 44211 no. exposed pairs = 2828 no. arc points = 20468 no. surface atoms = 939 nbur = 1265 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 474 mr = 3984 m= 1 mr = 95 m= 0 mr = 0 time to grow re-entrant surface = 8.0000013E-02 no. cavity mid-points inaccessible to solvent = 76 time to turn everything in is 0.1700000 number of dielectric boundary points 3732 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1897 ## 165 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 8114 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3835410E-08 -5.6826799E-08 midg,1,midg; midg,igrid,midg 8.2883584E-09 -6.3364368E-08 1,midg,midg; igrid,midg,midg -1.2469146E-08 -2.8650636E-08 gauss-seidel spectral radius is 0.9891717 estimated iterations to convergence 78 setup time was (sec) 0.3500000 now iterating at: 08:00:20 rms-change max change #iterations 0.1947098 27.48509 at 10iterations 2.2914330E-02 2.964428 at 20iterations 2.6914254E-03 0.3469715 at 30iterations 3.1450536E-04 4.7063828E-02 at 40iterations 3.7690443E-05 4.9953461E-03 at 50iterations finished qdiffx linear iterations at : 08:00:23 total time elapsed so far: 3.190000 # loops : 50 mean,max change (kT/e) : 3.7690443E-05 4.9953461E-03 energy calculations done at 3.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.320000 DelPhi exited at 08:00:23 3.321u 0.180s 0:03.77 92.8% 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 Sun Oct 9 2011 at 08:00:23 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: 325 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2204 !!! WARNING: NDP 385 has a net charge of -3.0000 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: 2.078913 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): 4.386000 50.00300 ymin,ymax (A): -25.23700 26.13600 zmin,zma (A): -19.74500 30.20500 x,y,z range (A): 45.61700 51.37300 49.95000 scale (grids/A): 2.078913 object centre (A): 27.19450 0.4495001 5.230000 number of atom coordinates read : 2204 total number of charged atoms : 2062 net assigned charge : -3.499990 assigned positive charge : 336.9805 centred at (gu) : 90.31541 93.05486 90.33589 assigned negative charge : -340.4807 centred at (gu) : 90.37500 93.29520 90.60596 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 77544 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20468 grid for indexing accessible points = 1.400000 m= 30652 mr = 53019 m= 6123 mr = 23118 m= 602 mr = 4121 m= 23 mr = 274 m= 0 mr = 3 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 1423 time to turn everything in is 0.3900000 number of dielectric boundary points 34409 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 91 iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 16393 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) : 0.6929710 object centre at (A) : 27.19450 0.4495001 5.230000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.8563072E-03 -3.7856795E-02 midg,1,midg; midg,igrid,midg 2.7641177E-02 -3.1039971E-03 1,midg,midg; igrid,midg,midg -4.1423426E-03 -2.8126236E-02 gauss-seidel spectral radius is 0.9988141 estimated iterations to convergence 230 setup time was (sec) 0.6100000 now iterating at: 08:00:24 rms-change max change #iterations 4.738595 176.0987 at 10iterations 2.322670 75.33923 at 20iterations 1.144632 36.74395 at 30iterations 0.5639827 18.01538 at 40iterations 0.2775244 8.190245 at 50iterations 0.1372999 4.182556 at 60iterations 6.7457236E-02 2.254571 at 70iterations 3.3134509E-02 1.081027 at 80iterations 1.6415263E-02 0.5819771 at 90iterations 8.0752205E-03 0.2560043 at 100iterations 3.9667091E-03 0.1139507 at 110iterations 1.9604762E-03 6.0028791E-02 at 120iterations finished qdiffx linear iterations at : 08:00:31 total time elapsed so far: 7.670000 # loops : 120 mean,max change (kT/e) : 1.9604762E-03 6.0028791E-02 energy calculations done at 7.670000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.800000 DelPhi exited at 08:00:31 7.799u 0.187s 0:08.24 96.7% 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 08:00:31 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: 325 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2204 !!! WARNING: NDP 385 has a net charge of -3.0000 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: 3.118370 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): 4.386000 50.00300 ymin,ymax (A): -25.23700 26.13600 zmin,zma (A): -19.74500 30.20500 x,y,z range (A): 45.61700 51.37300 49.95000 scale (grids/A): 3.118370 object centre (A): 27.19450 0.4495001 5.230000 number of atom coordinates read : 2204 total number of charged atoms : 2062 net assigned charge : -3.499990 assigned positive charge : 336.9805 centred at (gu) : 90.47314 94.58225 90.50363 assigned negative charge : -340.4807 centred at (gu) : 90.56245 94.94284 90.90889 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 178507 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20468 grid for indexing accessible points = 1.400000 m= 95093 mr = 127987 m= 39244 mr = 78543 m= 11615 mr = 32110 m= 2337 mr = 9055 m= 322 mr = 1650 m= 24 mr = 193 m= 0 mr = 6 time to grow re-entrant surface = 0.5900000 no. cavity mid-points inaccessible to solvent = 5009 time to turn everything in is 1.170000 number of dielectric boundary points 77598 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.260000 number of grid points assigned charge 16496 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) : 2.078913 object centre at (A) : 27.19450 0.4495001 5.230000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.2741815E-02 -0.2415683 midg,1,midg; midg,igrid,midg 0.8231508 8.9178808E-02 1,midg,midg; igrid,midg,midg -6.6149242E-02 -0.2560383 gauss-seidel spectral radius is 0.9992955 estimated iterations to convergence 297 setup time was (sec) 1.410000 now iterating at: 08:00:33 rms-change max change #iterations 10.63469 399.8915 at 10iterations 6.230680 149.0317 at 20iterations 3.635131 74.10004 at 30iterations 2.128282 52.57820 at 40iterations 1.242830 31.18891 at 50iterations 0.7259532 14.35904 at 60iterations 0.4236253 7.462461 at 70iterations 0.2469226 4.418695 at 80iterations 0.1438411 2.537424 at 90iterations 8.3929986E-02 1.451374 at 100iterations 4.8866235E-02 0.9362221 at 110iterations 2.8378578E-02 0.5515518 at 120iterations 1.6546646E-02 0.2832942 at 130iterations 9.6361870E-03 0.1710052 at 140iterations 5.5991691E-03 9.2747688E-02 at 150iterations 3.2676389E-03 5.6663513E-02 at 160iterations 1.9001365E-03 3.2278061E-02 at 170iterations 1.1075087E-03 1.9622326E-02 at 180iterations finished qdiffx linear iterations at : 08:00:44 total time elapsed so far: 12.82000 # loops : 180 mean,max change (kT/e) : 1.1075087E-03 1.9622326E-02 energy calculations done at 12.82000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.94000 DelPhi exited at 08:00:45 12.943u 0.212s 0:13.42 97.9% 0+0k 0+0io 0pf+0w