Sun Oct 9 14:59:51 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 14:59:51 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 = 1137 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: 0.8724849 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): 11.40800 52.21100 ymin,ymax (A): -52.70700 -16.92400 zmin,zma (A): -66.88700 -29.32900 x,y,z range (A): 40.80300 35.78300 37.55800 scale (grids/A): 0.8724849 object centre (A): 31.80950 -34.81550 -48.10800 number of atom coordinates read : 1137 total number of charged atoms : 1009 net assigned charge : 2.500005 assigned positive charge : 162.7672 centred at (gu) : 90.78583 88.27345 90.13021 assigned negative charge : -160.2671 centred at (gu) : 90.41976 88.15470 90.01237 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6199 nv = 96 ne = 84 npr = 23641 no. pairs analyzed = 23641 no. exposed pairs = 1480 no. arc points = 10614 no. surface atoms = 500 nbur = 637 mkacc time = 4.9999997E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 522 mr = 3426 m= 3 mr = 125 m= 0 mr = 0 time to grow re-entrant surface = 6.9999993E-02 no. cavity mid-points inaccessible to solvent = 53 time to turn everything in is 0.2100000 number of dielectric boundary points 3173 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 574 ## 63 charges are in solution ## iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 5207 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.8685290E-08 1.1165628E-06 midg,1,midg; midg,igrid,midg -1.4297191E-07 8.3414267E-07 1,midg,midg; igrid,midg,midg -1.2162292E-06 2.6080536E-06 gauss-seidel spectral radius is 0.9930373 estimated iterations to convergence 97 setup time was (sec) 0.4400000 now iterating at: 14:59:52 rms-change max change #iterations 0.3177920 49.68736 at 10iterations 5.7074744E-02 7.373920 at 20iterations 1.0203039E-02 1.517805 at 30iterations 1.8374257E-03 0.2464848 at 40iterations 3.2627105E-04 4.0868759E-02 at 50iterations finished qdiffx linear iterations at : 14:59:54 total time elapsed so far: 3.100000 # loops : 50 mean,max change (kT/e) : 3.2627105E-04 4.0868759E-02 energy calculations done at 3.100000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.300000 DelPhi exited at 14:59:55 3.305u 0.156s 0:03.73 92.4% 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 14:59:55 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 = 1137 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: 2.617455 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): 11.40800 52.21100 ymin,ymax (A): -52.70700 -16.92400 zmin,zma (A): -66.88700 -29.32900 x,y,z range (A): 40.80300 35.78300 37.55800 scale (grids/A): 2.617455 object centre (A): 31.80950 -34.81550 -48.10800 number of atom coordinates read : 1137 total number of charged atoms : 1009 net assigned charge : 2.500005 assigned positive charge : 162.7672 centred at (gu) : 92.35778 84.82064 90.39074 assigned negative charge : -160.2671 centred at (gu) : 91.25942 84.46408 90.03718 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 63308 reading accessible surface arcs data from file ARCDAT no. of arc points read = 10614 grid for indexing accessible points = 1.400000 m= 27412 mr = 43124 m= 6796 mr = 21149 m= 995 mr = 4822 m= 76 mr = 642 m= 3 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 1574 time to turn everything in is 0.5400000 number of dielectric boundary points 28811 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 8067 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) : 0.8724849 object centre at (A) : 31.80950 -34.81550 -48.10800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.6607938E-02 2.1574447E-02 midg,1,midg; midg,igrid,midg -8.6810710E-03 3.6462173E-02 1,midg,midg; igrid,midg,midg -7.1520112E-02 0.1556740 gauss-seidel spectral radius is 0.9990867 estimated iterations to convergence 261 setup time was (sec) 0.8300000 now iterating at: 14:59:56 rms-change max change #iterations 4.588709 238.3495 at 10iterations 2.468642 98.87796 at 20iterations 1.322600 47.21971 at 30iterations 0.7100875 20.90617 at 40iterations 0.3808487 12.25493 at 50iterations 0.2050125 6.675903 at 60iterations 0.1098359 3.530139 at 70iterations 5.9007622E-02 1.898158 at 80iterations 3.1890683E-02 0.9295101 at 90iterations 1.7018342E-02 0.5331554 at 100iterations 9.1228755E-03 0.2770691 at 110iterations 4.9126288E-03 0.1476212 at 120iterations finished qdiffx linear iterations at : 15:00:02 total time elapsed so far: 7.290000 # loops : 120 mean,max change (kT/e) : 4.9126288E-03 0.1476212 energy calculations done at 7.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.470000 DelPhi exited at 15:00:03 7.477u 0.158s 0:07.96 95.7% 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 15:00:03 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 = 1137 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: 3.926182 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): 11.40800 52.21100 ymin,ymax (A): -52.70700 -16.92400 zmin,zma (A): -66.88700 -29.32900 x,y,z range (A): 40.80300 35.78300 37.55800 scale (grids/A): 3.926182 object centre (A): 31.80950 -34.81550 -48.10800 number of atom coordinates read : 1137 total number of charged atoms : 1009 net assigned charge : 2.500005 assigned positive charge : 162.7672 centred at (gu) : 93.53677 82.23100 90.58617 assigned negative charge : -160.2671 centred at (gu) : 91.88914 81.69615 90.05585 start vw surface at 0.1200000 fill in re-entrant regions at 0.7900000 boundary points on vw surface= 145139 reading accessible surface arcs data from file ARCDAT no. of arc points read = 10614 grid for indexing accessible points = 1.400000 m= 80598 mr = 103214 m= 38316 mr = 67522 m= 13460 mr = 32240 m= 3680 mr = 10732 m= 786 mr = 2894 m= 134 mr = 580 m= 17 mr = 106 m= 0 mr = 14 time to grow re-entrant surface = 0.8000000 no. cavity mid-points inaccessible to solvent = 4899 time to turn everything in is 1.700000 number of dielectric boundary points 64828 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.840000 number of grid points assigned charge 8072 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) : 2.617455 object centre at (A) : 31.80950 -34.81550 -48.10800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2060048 0.1296241 midg,1,midg; midg,igrid,midg -0.1928402 0.1272614 1,midg,midg; igrid,midg,midg -0.7502969 1.337867 gauss-seidel spectral radius is 0.9993409 estimated iterations to convergence 307 setup time was (sec) 2.010000 now iterating at: 15:00:05 rms-change max change #iterations 9.398075 223.8459 at 10iterations 5.580493 118.2383 at 20iterations 3.314642 67.56084 at 30iterations 1.966167 34.17272 at 40iterations 1.169223 20.31047 at 50iterations 0.6926069 12.84988 at 60iterations 0.4106345 7.660622 at 70iterations 0.2434895 4.086421 at 80iterations 0.1445807 2.548028 at 90iterations 8.5496575E-02 1.508621 at 100iterations 5.0780222E-02 0.8726921 at 110iterations 3.0094758E-02 0.5507507 at 120iterations 1.7853104E-02 0.3173649 at 130iterations 1.0554859E-02 0.1857128 at 140iterations 6.2529328E-03 0.1092968 at 150iterations 3.7073030E-03 6.9000244E-02 at 160iterations 2.1981760E-03 3.9436340E-02 at 170iterations 1.3043771E-03 2.1812916E-02 at 180iterations finished qdiffx linear iterations at : 15:00:15 total time elapsed so far: 12.22000 # loops : 180 mean,max change (kT/e) : 1.3043771E-03 2.1812916E-02 energy calculations done at 12.22000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.41000 DelPhi exited at 15:00:16 12.417u 0.168s 0:12.95 97.0% 0+0k 0+0io 0pf+0w