Sun Oct 9 23:34:53 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 23:34:53 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2480 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: 0.5682090 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): 21.13000 68.24800 ymin,ymax (A): -21.39500 41.25800 zmin,zma (A): -19.58700 37.99300 x,y,z range (A): 47.11800 62.65300 57.58000 scale (grids/A): 0.5682090 object centre (A): 44.68900 9.931501 9.203000 number of atom coordinates read : 2480 total number of charged atoms : 2342 net assigned charge : 2.000005 assigned positive charge : 369.3132 centred at (gu) : 88.95696 88.51615 89.40845 assigned negative charge : -367.3138 centred at (gu) : 89.04942 88.54990 89.42072 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5177 nv = 96 ne = 84 npr = 49956 no. pairs analyzed = 49956 no. exposed pairs = 3148 no. arc points = 22375 no. surface atoms = 1063 nbur = 1417 mkacc time = 9.0000004E-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 = 1.540000 m= 216 mr = 2632 m= 4 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 2749 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2378 ## 332 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 6747 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.7708820E-10 1.0273549E-10 midg,1,midg; midg,igrid,midg 9.6371444E-10 -9.8805387E-11 1,midg,midg; igrid,midg,midg 1.7736714E-09 -6.7458367E-10 gauss-seidel spectral radius is 0.9839790 estimated iterations to convergence 65 setup time was (sec) 0.3900000 now iterating at: 23:34:54 rms-change max change #iterations 7.8060851E-02 12.67914 at 10iterations 5.7128207E-03 0.9046860 at 20iterations 4.2905236E-04 6.8355560E-02 at 30iterations 3.0861735E-05 5.7106018E-03 at 40iterations 2.3271627E-06 5.0735474E-04 at 50iterations finished qdiffx linear iterations at : 23:34:57 total time elapsed so far: 3.300000 # loops : 50 mean,max change (kT/e) : 2.3271627E-06 5.0735474E-04 energy calculations done at 3.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.420000 DelPhi exited at 23:34:57 3.427u 0.178s 0:03.99 89.9% 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 23:34:57 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2480 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: 1.704627 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): 21.13000 68.24800 ymin,ymax (A): -21.39500 41.25800 zmin,zma (A): -19.58700 37.99300 x,y,z range (A): 47.11800 62.65300 57.58000 scale (grids/A): 1.704627 object centre (A): 44.68900 9.931501 9.203000 number of atom coordinates read : 2480 total number of charged atoms : 2342 net assigned charge : 2.000005 assigned positive charge : 369.3132 centred at (gu) : 86.87038 85.54803 88.22484 assigned negative charge : -367.3138 centred at (gu) : 87.14808 85.64953 88.26198 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 56705 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22375 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 17169 mr = 37573 m= 1927 mr = 11837 m= 64 mr = 1036 m= 0 mr = 2 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 2052 time to turn everything in is 0.2900000 number of dielectric boundary points 25417 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 297 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 18133 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) : 0.5682090 object centre at (A) : 44.68900 9.931501 9.203000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.0972803E-02 4.6632160E-03 midg,1,midg; midg,igrid,midg 2.0283353E-02 1.3886845E-02 1,midg,midg; igrid,midg,midg 5.6917705E-03 -9.2799533E-03 gauss-seidel spectral radius is 0.9982767 estimated iterations to convergence 191 setup time was (sec) 0.5100000 now iterating at: 23:34:58 rms-change max change #iterations 3.218189 177.2962 at 10iterations 1.366557 60.34377 at 20iterations 0.5837972 24.16758 at 30iterations 0.2474515 9.259211 at 40iterations 0.1050710 4.027558 at 50iterations 4.4813130E-02 1.871824 at 60iterations 1.9140748E-02 0.6868668 at 70iterations 8.1319613E-03 0.2985255 at 80iterations 3.4674257E-03 0.1304169 at 90iterations 1.4717929E-03 5.6021690E-02 at 100iterations 6.2784890E-04 2.2811890E-02 at 110iterations 2.6805873E-04 1.0290146E-02 at 120iterations finished qdiffx linear iterations at : 23:35:05 total time elapsed so far: 7.650000 # loops : 120 mean,max change (kT/e) : 2.6805873E-04 1.0290146E-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) 7.800000 DelPhi exited at 23:35:06 7.804u 0.212s 0:08.28 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 23:35:06 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2480 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: 2.556941 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): 21.13000 68.24800 ymin,ymax (A): -21.39500 41.25800 zmin,zma (A): -19.58700 37.99300 x,y,z range (A): 47.11800 62.65300 57.58000 scale (grids/A): 2.556941 object centre (A): 44.68900 9.931501 9.203000 number of atom coordinates read : 2480 total number of charged atoms : 2342 net assigned charge : 2.000005 assigned positive charge : 369.3132 centred at (gu) : 85.30532 83.32198 87.33717 assigned negative charge : -367.3138 centred at (gu) : 85.72207 83.47424 87.39293 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 131554 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22375 grid for indexing accessible points = 1.400000 m= 59023 mr = 91875 m= 17436 mr = 46612 m= 3036 mr = 13212 m= 264 mr = 2065 m= 5 mr = 132 m= 0 mr = 0 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 7247 time to turn everything in is 0.6900000 number of dielectric boundary points 57422 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 12 iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 18727 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) : 1.704627 object centre at (A) : 44.68900 9.931501 9.203000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2218381 6.6581659E-02 midg,1,midg; midg,igrid,midg 0.4471097 0.2692667 1,midg,midg; igrid,midg,midg 0.1083938 -0.1393690 gauss-seidel spectral radius is 0.9991535 estimated iterations to convergence 271 setup time was (sec) 0.9300000 now iterating at: 23:35:07 rms-change max change #iterations 8.093615 317.3495 at 10iterations 4.504106 117.2835 at 20iterations 2.494969 56.98909 at 30iterations 1.381328 31.86706 at 40iterations 0.7669828 16.31073 at 50iterations 0.4232606 9.293305 at 60iterations 0.2337836 5.540411 at 70iterations 0.1289336 3.018821 at 80iterations 7.1108796E-02 1.570229 at 90iterations 3.9199971E-02 0.9574158 at 100iterations 2.1638449E-02 0.4663906 at 110iterations 1.1910663E-02 0.2452940 at 120iterations 6.5563987E-03 0.1479673 at 130iterations 3.6228732E-03 8.1316948E-02 at 140iterations 1.9972436E-03 4.1722298E-02 at 150iterations 1.0989172E-03 2.2846222E-02 at 160iterations 6.0694967E-04 1.3238907E-02 at 170iterations 3.3494207E-04 7.1134567E-03 at 180iterations finished qdiffx linear iterations at : 23:35:18 total time elapsed so far: 12.05000 # loops : 180 mean,max change (kT/e) : 3.3494207E-04 7.1134567E-03 energy calculations done at 12.05000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.18000 DelPhi exited at 23:35:19 12.181u 0.208s 0:12.75 97.0% 0+0k 0+0io 0pf+0w