Mon Oct 10 09:14:49 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 Mon Oct 10 2011 at 09:14:49 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: 226 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1963 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: 0.6068561 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): -24.05200 34.61100 ymin,ymax (A): -19.04800 20.62900 zmin,zma (A): -3.236000 39.05000 x,y,z range (A): 58.66300 39.67700 42.28600 scale (grids/A): 0.6068561 object centre (A): 5.279500 0.7904997 17.90700 number of atom coordinates read : 1963 total number of charged atoms : 1811 net assigned charge : 5.000011 assigned positive charge : 284.9490 centred at (gu) : 89.88314 90.23421 90.26732 assigned negative charge : -279.9493 centred at (gu) : 89.88316 90.31343 90.39482 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 4859 nv = 96 ne = 84 npr = 40802 no. pairs analyzed = 40802 no. exposed pairs = 2444 no. arc points = 17418 no. surface atoms = 843 nbur = 1120 mkacc time = 6.0000002E-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 = 1.456000 m= 212 mr = 2597 m= 3 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 6.0000002E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1600000 number of dielectric boundary points 2460 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1791 ## 211 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 5901 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.3847079E-09 -1.6125032E-09 midg,1,midg; midg,igrid,midg 4.9797961E-09 9.6000471E-11 1,midg,midg; igrid,midg,midg 2.7658080E-09 2.6274465E-09 gauss-seidel spectral radius is 0.9858899 estimated iterations to convergence 69 setup time was (sec) 0.3500000 now iterating at: 09:14:49 rms-change max change #iterations 9.8382145E-02 20.03416 at 10iterations 8.6863628E-03 1.517196 at 20iterations 7.4334606E-04 0.1451645 at 30iterations 6.2799438E-05 1.2298584E-02 at 40iterations 5.5785767E-06 8.8024139E-04 at 50iterations finished qdiffx linear iterations at : 09:14:52 total time elapsed so far: 3.230000 # loops : 50 mean,max change (kT/e) : 5.5785767E-06 8.8024139E-04 energy calculations done at 3.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.370000 DelPhi exited at 09:14:53 3.371u 0.173s 0:03.94 89.8% 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 Mon Oct 10 2011 at 09:14:53 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: 226 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1963 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.820568 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): -24.05200 34.61100 ymin,ymax (A): -19.04800 20.62900 zmin,zma (A): -3.236000 39.05000 x,y,z range (A): 58.66300 39.67700 42.28600 scale (grids/A): 1.820568 object centre (A): 5.279500 0.7904997 17.90700 number of atom coordinates read : 1963 total number of charged atoms : 1811 net assigned charge : 5.000011 assigned positive charge : 284.9490 centred at (gu) : 89.64944 90.70277 90.80199 assigned negative charge : -279.9493 centred at (gu) : 89.64958 90.94057 91.18481 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 52616 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17418 grid for indexing accessible points = 1.400000 m= 18362 mr = 35687 m= 2379 mr = 13633 m= 85 mr = 1335 m= 2 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2700000 number of dielectric boundary points 22772 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 139 iepsmp to db, and charging done at 0.3400000 number of grid points assigned charge 14161 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) : 0.6068561 object centre at (A) : 5.279500 0.7904997 17.90700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.3902787E-03 -5.7024840E-04 midg,1,midg; midg,igrid,midg 5.9657688E-03 1.9170931E-03 1,midg,midg; igrid,midg,midg 4.3877166E-02 3.3307236E-02 gauss-seidel spectral radius is 0.9984319 estimated iterations to convergence 200 setup time was (sec) 0.4800000 now iterating at: 09:14:53 rms-change max change #iterations 3.247564 183.2519 at 10iterations 1.431482 54.32544 at 20iterations 0.6364593 26.14350 at 30iterations 0.2813970 11.62461 at 40iterations 0.1249244 4.815819 at 50iterations 5.5144072E-02 2.424725 at 60iterations 2.4614312E-02 0.8690376 at 70iterations 1.0882769E-02 0.4711189 at 80iterations 4.8182756E-03 0.1799297 at 90iterations 2.1292239E-03 8.4711075E-02 at 100iterations 9.4587053E-04 4.2633057E-02 at 110iterations 4.2134314E-04 1.6391754E-02 at 120iterations finished qdiffx linear iterations at : 09:15:00 total time elapsed so far: 7.410000 # loops : 120 mean,max change (kT/e) : 4.2134314E-04 1.6391754E-02 energy calculations done at 7.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.560000 DelPhi exited at 09:15:01 7.558u 0.187s 0:08.01 96.5% 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 Mon Oct 10 2011 at 09:15:01 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: 226 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1963 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.730852 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): -24.05200 34.61100 ymin,ymax (A): -19.04800 20.62900 zmin,zma (A): -3.236000 39.05000 x,y,z range (A): 58.66300 39.67700 42.28600 scale (grids/A): 2.730852 object centre (A): 5.279500 0.7904997 17.90700 number of atom coordinates read : 1963 total number of charged atoms : 1811 net assigned charge : 5.000011 assigned positive charge : 284.9490 centred at (gu) : 89.47422 91.05405 91.20303 assigned negative charge : -279.9493 centred at (gu) : 89.47448 91.41081 91.77724 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 121483 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17418 grid for indexing accessible points = 1.400000 m= 60271 mr = 86500 m= 20336 mr = 49367 m= 3934 mr = 16421 m= 332 mr = 2740 m= 7 mr = 195 m= 0 mr = 0 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6600000 number of dielectric boundary points 51140 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 14488 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) : 1.820568 object centre at (A) : 5.279500 0.7904997 17.90700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.6538064E-02 2.9810321E-02 midg,1,midg; midg,igrid,midg 4.0761717E-02 4.8564680E-02 1,midg,midg; igrid,midg,midg 0.6134262 0.3589453 gauss-seidel spectral radius is 0.9991856 estimated iterations to convergence 277 setup time was (sec) 0.8800000 now iterating at: 09:15:02 rms-change max change #iterations 7.743064 317.1615 at 10iterations 4.382064 119.5949 at 20iterations 2.470896 60.71114 at 30iterations 1.381247 34.23917 at 40iterations 0.7747618 17.79618 at 50iterations 0.4335064 9.619680 at 60iterations 0.2416588 5.181190 at 70iterations 0.1344229 2.988441 at 80iterations 7.5402312E-02 1.713596 at 90iterations 4.1947953E-02 0.9540405 at 100iterations 2.3382593E-02 0.5304174 at 110iterations 1.3084925E-02 0.2772217 at 120iterations 7.2814873E-03 0.1715744 at 130iterations 4.0669548E-03 8.4693909E-02 at 140iterations 2.2674231E-03 4.5471191E-02 at 150iterations 1.2645851E-03 2.6058197E-02 at 160iterations 7.0448895E-04 1.4554977E-02 at 170iterations 3.9326749E-04 1.0010719E-02 at 180iterations finished qdiffx linear iterations at : 09:15:12 total time elapsed so far: 11.54000 # loops : 180 mean,max change (kT/e) : 3.9326749E-04 1.0010719E-02 energy calculations done at 11.54000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.67000 DelPhi exited at 09:15:13 11.672u 0.199s 0:12.27 96.6% 0+0k 0+0io 0pf+0w