Sat Oct 8 16:23:25 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 Sat Oct 8 2011 at 16:23:25 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 = 2395 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5842387 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): -2.480000 46.55700 ymin,ymax (A): -15.54100 29.74100 zmin,zma (A): -18.98200 41.95200 x,y,z range (A): 49.03700 45.28200 60.93400 scale (grids/A): 0.5842387 object centre (A): 22.03850 7.100000 11.48500 number of atom coordinates read : 2395 total number of charged atoms : 2288 net assigned charge : 4.000001 assigned positive charge : 352.0741 centred at (gu) : 90.20082 88.72989 88.90185 assigned negative charge : -348.0747 centred at (gu) : 90.23212 88.86160 88.92675 start vw surface at 0.1600000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 5190 nv = 96 ne = 84 npr = 49647 no. pairs analyzed = 49647 no. exposed pairs = 2887 no. arc points = 19822 no. surface atoms = 986 nbur = 1409 mkacc time = 0.1300000 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= 213 mr = 2788 m= 0 mr = 19 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 19 time to turn everything in is 0.3300000 number of dielectric boundary points 2596 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2053 ## 217 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 6802 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8800739E-09 3.7704820E-10 midg,1,midg; midg,igrid,midg 4.7633635E-09 -1.2319251E-09 1,midg,midg; igrid,midg,midg 1.5144286E-09 3.6227119E-10 gauss-seidel spectral radius is 0.9848236 estimated iterations to convergence 67 setup time was (sec) 0.6000000 now iterating at: 16:23:25 rms-change max change #iterations 8.8398904E-02 18.05255 at 10iterations 7.1083321E-03 1.255015 at 20iterations 6.0548133E-04 0.1265545 at 30iterations 7.5201999E-05 1.6650677E-02 at 40iterations 1.5692034E-05 3.8313866E-03 at 50iterations finished qdiffx linear iterations at : 16:23:29 total time elapsed so far: 3.890000 # loops : 50 mean,max change (kT/e) : 1.5692034E-05 3.8313866E-03 energy calculations done at 3.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.070000 DelPhi exited at 16:23:29 4.074u 0.260s 0:04.63 93.5% 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 Sat Oct 8 2011 at 16:23:29 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 = 2395 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.752716 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): -2.480000 46.55700 ymin,ymax (A): -15.54100 29.74100 zmin,zma (A): -18.98200 41.95200 x,y,z range (A): 49.03700 45.28200 60.93400 scale (grids/A): 1.752716 object centre (A): 22.03850 7.100000 11.48500 number of atom coordinates read : 2395 total number of charged atoms : 2288 net assigned charge : 4.000001 assigned positive charge : 352.0741 centred at (gu) : 90.60197 86.18905 86.70509 assigned negative charge : -348.0747 centred at (gu) : 90.69621 86.58457 86.78004 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 57941 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19822 grid for indexing accessible points = 1.400000 m= 18406 mr = 40245 m= 2275 mr = 13214 m= 81 mr = 1304 m= 0 mr = 14 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 1913 time to turn everything in is 0.5300000 number of dielectric boundary points 23926 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 177 iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 17827 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) : 0.5842387 object centre at (A) : 22.03850 7.100000 11.48500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9668901E-02 1.5893068E-02 midg,1,midg; midg,igrid,midg 1.3882237E-02 -2.5245354E-03 1,midg,midg; igrid,midg,midg 2.6506200E-03 -1.6064676E-02 gauss-seidel spectral radius is 0.9983602 estimated iterations to convergence 196 setup time was (sec) 0.8200000 now iterating at: 16:23:30 rms-change max change #iterations 3.342236 162.5195 at 10iterations 1.463361 64.51611 at 20iterations 0.6355927 23.27065 at 30iterations 0.2776141 10.35067 at 40iterations 0.1212486 4.792360 at 50iterations 5.2737795E-02 1.967595 at 60iterations 2.2981657E-02 0.8542023 at 70iterations 1.0000907E-02 0.3654299 at 80iterations 4.3868124E-03 0.1530914 at 90iterations 1.9214147E-03 7.5307846E-02 at 100iterations 8.4330252E-04 3.3828735E-02 at 110iterations 3.7158551E-04 1.5039444E-02 at 120iterations finished qdiffx linear iterations at : 16:23:39 total time elapsed so far: 9.070000 # loops : 120 mean,max change (kT/e) : 3.7158551E-04 1.5039444E-02 energy calculations done at 9.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.260000 DelPhi exited at 16:23:39 9.261u 0.300s 0:09.92 96.3% 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 Sat Oct 8 2011 at 16:23:39 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 = 2395 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.629074 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): -2.480000 46.55700 ymin,ymax (A): -15.54100 29.74100 zmin,zma (A): -18.98200 41.95200 x,y,z range (A): 49.03700 45.28200 60.93400 scale (grids/A): 2.629074 object centre (A): 22.03850 7.100000 11.48500 number of atom coordinates read : 2395 total number of charged atoms : 2288 net assigned charge : 4.000001 assigned positive charge : 352.0741 centred at (gu) : 90.90269 84.28345 85.05753 assigned negative charge : -348.0747 centred at (gu) : 91.04433 84.87681 85.17010 start vw surface at 0.1500000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 134474 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19822 grid for indexing accessible points = 1.400000 m= 62580 mr = 98046 m= 19618 mr = 50343 m= 3839 mr = 15526 m= 356 mr = 2757 m= 4 mr = 194 m= 0 mr = 0 time to grow re-entrant surface = 0.7200000 no. cavity mid-points inaccessible to solvent = 6257 time to turn everything in is 1.270000 number of dielectric boundary points 54005 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 1.420000 number of grid points assigned charge 18293 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) : 1.752716 object centre at (A) : 22.03850 7.100000 11.48500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2379952 0.4777767 midg,1,midg; midg,igrid,midg 0.1547419 -3.7444968E-02 1,midg,midg; igrid,midg,midg 3.8965218E-02 -0.2790803 gauss-seidel spectral radius is 0.9991722 estimated iterations to convergence 274 setup time was (sec) 1.590000 now iterating at: 16:23:41 rms-change max change #iterations 8.314416 269.4907 at 10iterations 4.713672 136.8327 at 20iterations 2.664016 61.63105 at 30iterations 1.497855 33.56109 at 40iterations 0.8417528 18.88943 at 50iterations 0.4723652 10.69123 at 60iterations 0.2638013 5.967987 at 70iterations 0.1476170 3.528861 at 80iterations 8.2386144E-02 1.750057 at 90iterations 4.6025060E-02 0.9919643 at 100iterations 2.5615774E-02 0.5271912 at 110iterations 1.4311734E-02 0.2987919 at 120iterations 7.9516200E-03 0.1678886 at 130iterations 4.4413349E-03 8.8935852E-02 at 140iterations 2.4735292E-03 5.0353765E-02 at 150iterations 1.3791196E-03 3.0284882E-02 at 160iterations 7.7312824E-04 1.7999649E-02 at 170iterations 4.3394833E-04 8.8825226E-03 at 180iterations finished qdiffx linear iterations at : 16:23:54 total time elapsed so far: 14.74000 # loops : 180 mean,max change (kT/e) : 4.3394833E-04 8.8825226E-03 energy calculations done at 14.74000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.92000 DelPhi exited at 16:23:55 14.925u 0.304s 0:15.55 97.8% 0+0k 0+0io 0pf+0w