Sun Oct 9 22:24:11 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 22:24:11 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 = 2583 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: 0.6407257 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): 8.228000 62.83400 ymin,ymax (A): -38.76300 16.79900 zmin,zma (A): -3.892000 49.13000 x,y,z range (A): 54.60600 55.56200 53.02200 scale (grids/A): 0.6407257 object centre (A): 35.53100 -10.98200 22.61900 number of atom coordinates read : 2583 total number of charged atoms : 2438 net assigned charge : 5.000012 assigned positive charge : 389.6449 centred at (gu) : 90.27105 91.19551 90.22705 assigned negative charge : -384.6457 centred at (gu) : 90.31485 91.26198 90.25706 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6979 nv = 96 ne = 84 npr = 52403 no. pairs analyzed = 52403 no. exposed pairs = 3176 no. arc points = 22270 no. surface atoms = 1077 nbur = 1506 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 388 mr = 3774 m= 0 mr = 52 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 24 time to turn everything in is 0.2000000 number of dielectric boundary points 3541 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2242 ## 228 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 8482 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0563261E-08 4.1931885E-09 midg,1,midg; midg,igrid,midg 1.1912491E-08 -5.6458860E-10 1,midg,midg; igrid,midg,midg 1.1984572E-08 2.4933793E-09 gauss-seidel spectral radius is 0.9873787 estimated iterations to convergence 73 setup time was (sec) 0.3900000 now iterating at: 22:24:12 rms-change max change #iterations 0.1463111 24.86333 at 10iterations 1.4425556E-02 2.311504 at 20iterations 1.4472975E-03 0.2169781 at 30iterations 1.4340265E-04 1.8985748E-02 at 40iterations 1.4755362E-05 2.1286011E-03 at 50iterations finished qdiffx linear iterations at : 22:24:14 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 1.4755362E-05 2.1286011E-03 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.420000 DelPhi exited at 22:24:15 3.423u 0.191s 0:03.97 90.9% 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 22:24:15 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 = 2583 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: 1.922177 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): 8.228000 62.83400 ymin,ymax (A): -38.76300 16.79900 zmin,zma (A): -3.892000 49.13000 x,y,z range (A): 54.60600 55.56200 53.02200 scale (grids/A): 1.922177 object centre (A): 35.53100 -10.98200 22.61900 number of atom coordinates read : 2583 total number of charged atoms : 2438 net assigned charge : 5.000012 assigned positive charge : 389.6449 centred at (gu) : 90.81239 93.58606 90.68058 assigned negative charge : -384.6457 centred at (gu) : 90.94445 93.78577 90.77093 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 75433 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22270 grid for indexing accessible points = 1.400000 m= 25883 mr = 51774 m= 4194 mr = 18685 m= 296 mr = 2634 m= 4 mr = 135 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 1505 time to turn everything in is 0.3800000 number of dielectric boundary points 32582 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 170 iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 19212 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) : 0.6407257 object centre at (A) : 35.53100 -10.98200 22.61900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.8560817E-02 -5.3750169E-03 midg,1,midg; midg,igrid,midg -7.1229171E-03 2.4109386E-02 1,midg,midg; igrid,midg,midg -2.7808531E-03 5.2057719E-03 gauss-seidel spectral radius is 0.9986529 estimated iterations to convergence 216 setup time was (sec) 0.6000000 now iterating at: 22:24:16 rms-change max change #iterations 4.238913 196.8756 at 10iterations 1.995929 62.60141 at 20iterations 0.9425431 32.55098 at 30iterations 0.4417901 13.87831 at 40iterations 0.2068845 6.378265 at 50iterations 9.7742960E-02 3.298963 at 60iterations 4.5931686E-02 1.391730 at 70iterations 2.1667812E-02 0.6821692 at 80iterations 1.0185339E-02 0.3285899 at 90iterations 4.7787162E-03 0.1644012 at 100iterations 2.2551231E-03 6.9540024E-02 at 110iterations 1.0585635E-03 3.4262657E-02 at 120iterations finished qdiffx linear iterations at : 22:24:23 total time elapsed so far: 7.800000 # loops : 120 mean,max change (kT/e) : 1.0585635E-03 3.4262657E-02 energy calculations done at 7.800000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.920000 DelPhi exited at 22:24:23 7.924u 0.206s 0:08.50 95.5% 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 Sun Oct 9 2011 at 22:24:24 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 = 2583 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: 2.883266 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): 8.228000 62.83400 ymin,ymax (A): -38.76300 16.79900 zmin,zma (A): -3.892000 49.13000 x,y,z range (A): 54.60600 55.56200 53.02200 scale (grids/A): 2.883266 object centre (A): 35.53100 -10.98200 22.61900 number of atom coordinates read : 2583 total number of charged atoms : 2438 net assigned charge : 5.000012 assigned positive charge : 389.6449 centred at (gu) : 91.21844 95.37894 91.02065 assigned negative charge : -384.6457 centred at (gu) : 91.41660 95.67858 91.15641 start vw surface at 0.1000000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 174685 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22270 grid for indexing accessible points = 1.400000 m= 84891 mr = 125614 m= 29508 mr = 68820 m= 7614 mr = 23232 m= 1295 mr = 5818 m= 91 mr = 962 m= 3 mr = 48 m= 0 mr = 0 time to grow re-entrant surface = 0.5500001 no. cavity mid-points inaccessible to solvent = 4939 time to turn everything in is 0.9900000 number of dielectric boundary points 73593 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.070000 number of grid points assigned charge 19504 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) : 1.922177 object centre at (A) : 35.53100 -10.98200 22.61900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3827817 -0.1974393 midg,1,midg; midg,igrid,midg -0.2275283 0.3015998 1,midg,midg; igrid,midg,midg 4.8304554E-02 -0.1317874 gauss-seidel spectral radius is 0.9992670 estimated iterations to convergence 291 setup time was (sec) 1.220000 now iterating at: 22:24:25 rms-change max change #iterations 9.984917 373.0353 at 10iterations 5.822927 135.7440 at 20iterations 3.380015 66.36505 at 30iterations 1.956585 39.96103 at 40iterations 1.130742 21.11966 at 50iterations 0.6516209 13.73879 at 60iterations 0.3771937 7.458545 at 70iterations 0.2172201 4.210670 at 80iterations 0.1251568 2.487367 at 90iterations 7.2122172E-02 1.441278 at 100iterations 4.1431367E-02 0.7216606 at 110iterations 2.3847949E-02 0.4763308 at 120iterations 1.3747009E-02 0.2431269 at 130iterations 7.9167942E-03 0.1335831 at 140iterations 4.5504356E-03 7.8414917E-02 at 150iterations 2.6191885E-03 5.1593781E-02 at 160iterations 1.5063654E-03 2.7065277E-02 at 170iterations 8.6834992E-04 1.5762329E-02 at 180iterations finished qdiffx linear iterations at : 22:24:36 total time elapsed so far: 12.70000 # loops : 180 mean,max change (kT/e) : 8.6834992E-04 1.5762329E-02 energy calculations done at 12.70000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.84000 DelPhi exited at 22:24:37 12.840u 0.218s 0:13.37 97.6% 0+0k 0+0io 0pf+0w