Sun Oct 16 15:15:34 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 16 2011 at 15:15:34 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: 313 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2556 !!! WARNING: GLM 165 has a net charge of -0.0940 !!! WARNING: SEP 167 has a net charge of -0.4750 !!! WARNING: HIR 207 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6476849 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): -56.15800 -1.193000 ymin,ymax (A): -26.75400 24.12600 zmin,zma (A): -2.653000 44.38200 x,y,z range (A): 54.96500 50.88000 47.03500 scale (grids/A): 0.6476849 object centre (A): -28.67550 -1.314000 20.86450 number of atom coordinates read : 2556 total number of charged atoms : 2404 net assigned charge : -3.054993 assigned positive charge : 378.9470 centred at (gu) : 90.59663 90.37835 88.77197 assigned negative charge : -382.0025 centred at (gu) : 90.51246 90.30103 88.61574 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7417 nv = 96 ne = 84 npr = 51799 no. pairs analyzed = 51799 no. exposed pairs = 3180 no. arc points = 22116 no. surface atoms = 1083 nbur = 1473 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 402 mr = 4243 m= 4 mr = 59 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 7 time to turn everything in is 0.3000000 number of dielectric boundary points 3521 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2156 ## 191 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8638 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.6100566E-08 1.2496688E-08 midg,1,midg; midg,igrid,midg -1.5047918E-08 5.9852141E-09 1,midg,midg; igrid,midg,midg -1.5235141E-08 7.3715425E-09 gauss-seidel spectral radius is 0.9876477 estimated iterations to convergence 74 setup time was (sec) 0.5000000 now iterating at: 15:15:34 rms-change max change #iterations 0.1477581 22.13326 at 10iterations 1.5119278E-02 2.257774 at 20iterations 1.5477777E-03 0.2208023 at 30iterations 1.5996712E-04 2.2159576E-02 at 40iterations 1.7126509E-05 2.3689270E-03 at 50iterations finished qdiffx linear iterations at : 15:15:37 total time elapsed so far: 2.950000 # loops : 50 mean,max change (kT/e) : 1.7126509E-05 2.3689270E-03 energy calculations done at 2.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.120000 DelPhi exited at 15:15:37 3.126u 0.156s 0:03.53 92.6% 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 16 2011 at 15:15:37 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: 313 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2556 !!! WARNING: GLM 165 has a net charge of -0.0940 !!! WARNING: SEP 167 has a net charge of -0.4750 !!! WARNING: HIR 207 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.943055 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): -56.15800 -1.193000 ymin,ymax (A): -26.75400 24.12600 zmin,zma (A): -2.653000 44.38200 x,y,z range (A): 54.96500 50.88000 47.03500 scale (grids/A): 1.943055 object centre (A): -28.67550 -1.314000 20.86450 number of atom coordinates read : 2556 total number of charged atoms : 2404 net assigned charge : -3.054993 assigned positive charge : 378.9470 centred at (gu) : 91.78947 91.13476 86.31558 assigned negative charge : -382.0025 centred at (gu) : 91.53747 90.90284 85.84700 start vw surface at 0.1400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 79205 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22116 grid for indexing accessible points = 1.400000 m= 30354 mr = 55649 m= 5111 mr = 23306 m= 363 mr = 3442 m= 5 mr = 157 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 821 time to turn everything in is 0.5400000 number of dielectric boundary points 32484 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 135 iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 18966 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) : 0.6476849 object centre at (A) : -28.67550 -1.314000 20.86450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9762449E-02 2.1209957E-02 midg,1,midg; midg,igrid,midg -4.3343548E-02 -2.7790200E-02 1,midg,midg; igrid,midg,midg -1.6875481E-02 -3.6401186E-02 gauss-seidel spectral radius is 0.9986858 estimated iterations to convergence 219 setup time was (sec) 0.8200000 now iterating at: 15:15:38 rms-change max change #iterations 4.361934 187.3959 at 10iterations 2.082418 69.67749 at 20iterations 0.9875005 31.10827 at 30iterations 0.4701409 15.64418 at 40iterations 0.2237126 7.355003 at 50iterations 0.1062053 3.416281 at 60iterations 5.0486464E-02 1.476860 at 70iterations 2.4131354E-02 0.8401871 at 80iterations 1.1379581E-02 0.3447170 at 90iterations 5.4222671E-03 0.1611204 at 100iterations 2.5907462E-03 9.4806671E-02 at 110iterations 1.2370781E-03 3.5964966E-02 at 120iterations finished qdiffx linear iterations at : 15:15:44 total time elapsed so far: 6.880000 # loops : 120 mean,max change (kT/e) : 1.2370781E-03 3.5964966E-02 energy calculations done at 6.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.060000 DelPhi exited at 15:15:45 7.059u 0.170s 0:07.51 96.1% 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 Sun Oct 16 2011 at 15:15:45 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: 313 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2556 !!! WARNING: GLM 165 has a net charge of -0.0940 !!! WARNING: SEP 167 has a net charge of -0.4750 !!! WARNING: HIR 207 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.914582 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): -56.15800 -1.193000 ymin,ymax (A): -26.75400 24.12600 zmin,zma (A): -2.653000 44.38200 x,y,z range (A): 54.96500 50.88000 47.03500 scale (grids/A): 2.914582 object centre (A): -28.67550 -1.314000 20.86450 number of atom coordinates read : 2556 total number of charged atoms : 2404 net assigned charge : -3.054993 assigned positive charge : 378.9470 centred at (gu) : 92.68404 91.70190 84.47326 assigned negative charge : -382.0025 centred at (gu) : 92.30599 91.35420 83.77049 start vw surface at 0.1500000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 182838 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22116 grid for indexing accessible points = 1.400000 m= 96691 mr = 134193 m= 37127 mr = 80981 m= 9543 mr = 30791 m= 1588 mr = 7571 m= 101 mr = 1151 m= 3 mr = 45 m= 0 mr = 0 time to grow re-entrant surface = 0.8400000 no. cavity mid-points inaccessible to solvent = 2762 time to turn everything in is 1.410000 number of dielectric boundary points 73159 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.530000 number of grid points assigned charge 19232 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) : 1.943055 object centre at (A) : -28.67550 -1.314000 20.86450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3670824 0.1480276 midg,1,midg; midg,igrid,midg -0.5224963 -0.3728557 1,midg,midg; igrid,midg,midg -8.0330290E-02 -0.4026060 gauss-seidel spectral radius is 0.9992711 estimated iterations to convergence 292 setup time was (sec) 1.690000 now iterating at: 15:15:47 rms-change max change #iterations 10.10609 384.3170 at 10iterations 5.888474 133.5344 at 20iterations 3.402462 65.90461 at 30iterations 1.971541 45.26196 at 40iterations 1.136689 21.09165 at 50iterations 0.6583919 11.68607 at 60iterations 0.3794133 6.940286 at 70iterations 0.2189254 3.666378 at 80iterations 0.1261580 2.325062 at 90iterations 7.2734334E-02 1.198743 at 100iterations 4.1905373E-02 0.7160225 at 110iterations 2.4182595E-02 0.4056462 at 120iterations 1.3911279E-02 0.2308021 at 130iterations 8.0410792E-03 0.1366367 at 140iterations 4.6440060E-03 8.3930969E-02 at 150iterations 2.6765736E-03 4.6176910E-02 at 160iterations 1.5448524E-03 2.5604248E-02 at 170iterations 8.8962243E-04 1.5183598E-02 at 180iterations finished qdiffx linear iterations at : 15:15:57 total time elapsed so far: 11.99000 # loops : 180 mean,max change (kT/e) : 8.8962243E-04 1.5183598E-02 energy calculations done at 11.99000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.16000 DelPhi exited at 15:15:58 12.164u 0.179s 0:12.65 97.4% 0+0k 0+0io 0pf+0w