Mon Oct 10 14:06:15 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 14:06:15 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3107 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5966647 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): 1.996000 61.66100 ymin,ymax (A): -21.70900 26.76200 zmin,zma (A): -9.971000 45.08700 x,y,z range (A): 59.66500 48.47100 55.05800 scale (grids/A): 0.5966647 object centre (A): 31.82850 2.526500 17.55800 number of atom coordinates read : 3107 total number of charged atoms : 2964 net assigned charge : 2.000008 assigned positive charge : 462.6611 centred at (gu) : 90.15092 89.28240 91.04976 assigned negative charge : -460.6622 centred at (gu) : 90.13934 89.23964 91.08188 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7254 nv = 96 ne = 84 npr = 64039 no. pairs analyzed = 64039 no. exposed pairs = 3626 no. arc points = 25609 no. surface atoms = 1204 nbur = 1903 mkacc time = 0.1400000 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= 326 mr = 4056 m= 2 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 6 time to turn everything in is 0.3300000 number of dielectric boundary points 3498 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2622 ## 284 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 9240 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.6099705E-09 -6.0292010E-10 midg,1,midg; midg,igrid,midg -1.0489737E-09 2.0836071E-09 1,midg,midg; igrid,midg,midg 3.3233663E-10 1.2887856E-09 gauss-seidel spectral radius is 0.9855023 estimated iterations to convergence 68 setup time was (sec) 0.6200000 now iterating at: 14:06:16 rms-change max change #iterations 0.1144942 18.83112 at 10iterations 1.1343197E-02 1.706543 at 20iterations 2.4071534E-03 0.5125351 at 30iterations 7.9592440E-04 0.1777420 at 40iterations 2.7606703E-04 6.1935425E-02 at 50iterations finished qdiffx linear iterations at : 14:06:20 total time elapsed so far: 4.130000 # loops : 50 mean,max change (kT/e) : 2.7606703E-04 6.1935425E-02 energy calculations done at 4.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.300000 DelPhi exited at 14:06:20 4.308u 0.245s 0:05.02 90.4% 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 Mon Oct 10 2011 at 14:06:20 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3107 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.789994 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): 1.996000 61.66100 ymin,ymax (A): -21.70900 26.76200 zmin,zma (A): -9.971000 45.08700 x,y,z range (A): 59.66500 48.47100 55.05800 scale (grids/A): 1.789994 object centre (A): 31.82850 2.526500 17.55800 number of atom coordinates read : 3107 total number of charged atoms : 2964 net assigned charge : 2.000008 assigned positive charge : 462.6611 centred at (gu) : 90.45168 87.84671 93.14866 assigned negative charge : -460.6622 centred at (gu) : 90.41774 87.71844 93.24532 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 80203 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25609 grid for indexing accessible points = 1.400000 m= 27053 mr = 56957 m= 3306 mr = 19649 m= 136 mr = 1895 m= 0 mr = 34 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 433 time to turn everything in is 0.5700000 number of dielectric boundary points 32163 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 214 iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 23081 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) : 0.5966647 object centre at (A) : 31.82850 2.526500 17.55800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.8786231E-03 -1.8657520E-02 midg,1,midg; midg,igrid,midg -2.6794977E-03 7.9799723E-03 1,midg,midg; igrid,midg,midg 2.8251689E-02 1.2189632E-02 gauss-seidel spectral radius is 0.9985068 estimated iterations to convergence 205 setup time was (sec) 0.9000000 now iterating at: 14:06:21 rms-change max change #iterations 4.109619 179.6653 at 10iterations 1.847598 62.91139 at 20iterations 0.8386267 30.27621 at 30iterations 0.3795508 14.15533 at 40iterations 0.1731108 5.712014 at 50iterations 7.8583531E-02 2.627409 at 60iterations 3.5965383E-02 1.204588 at 70iterations 1.6815903E-02 0.5248260 at 80iterations 7.9997480E-03 0.2908211 at 90iterations 4.0245252E-03 0.1580734 at 100iterations 2.1862246E-03 8.7310791E-02 at 110iterations 1.2802334E-03 5.5046082E-02 at 120iterations finished qdiffx linear iterations at : 14:06:30 total time elapsed so far: 9.240000 # loops : 120 mean,max change (kT/e) : 1.2802334E-03 5.5046082E-02 energy calculations done at 9.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.420000 DelPhi exited at 14:06:30 9.427u 0.253s 0:09.99 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 Mon Oct 10 2011 at 14:06:30 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3107 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.684991 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): 1.996000 61.66100 ymin,ymax (A): -21.70900 26.76200 zmin,zma (A): -9.971000 45.08700 x,y,z range (A): 59.66500 48.47100 55.05800 scale (grids/A): 2.684991 object centre (A): 31.82850 2.526500 17.55800 number of atom coordinates read : 3107 total number of charged atoms : 2964 net assigned charge : 2.000008 assigned positive charge : 462.6611 centred at (gu) : 90.67754 86.76971 94.72274 assigned negative charge : -460.6622 centred at (gu) : 90.62658 86.57757 94.86781 start vw surface at 0.1500000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 186521 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25609 grid for indexing accessible points = 1.400000 m= 91432 mr = 138627 m= 28437 mr = 74643 m= 5578 mr = 22399 m= 565 mr = 4074 m= 27 mr = 338 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.8500000 no. cavity mid-points inaccessible to solvent = 1611 time to turn everything in is 1.480000 number of dielectric boundary points 72470 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.630000 number of grid points assigned charge 23710 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) : 1.789994 object centre at (A) : 31.82850 2.526500 17.55800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.5326513E-02 -0.1550261 midg,1,midg; midg,igrid,midg -4.7939938E-02 0.1088044 1,midg,midg; igrid,midg,midg 0.5401693 0.1956703 gauss-seidel spectral radius is 0.9992304 estimated iterations to convergence 285 setup time was (sec) 1.810000 now iterating at: 14:06:32 rms-change max change #iterations 9.899240 341.1390 at 10iterations 5.710015 140.8099 at 20iterations 3.285393 64.29848 at 30iterations 1.884506 38.84753 at 40iterations 1.075575 19.63710 at 50iterations 0.6150351 12.03179 at 60iterations 0.3509881 6.636639 at 70iterations 0.2002389 3.677217 at 80iterations 0.1140931 2.116096 at 90iterations 6.4918458E-02 1.226295 at 100iterations 3.7053786E-02 0.6637897 at 110iterations 2.1274822E-02 0.3828125 at 120iterations 1.2247810E-02 0.2184544 at 130iterations 7.1380492E-03 0.1387482 at 140iterations 4.2607901E-03 8.3435059E-02 at 150iterations 2.6345341E-03 5.5103302E-02 at 160iterations 1.7050807E-03 3.9718628E-02 at 170iterations 1.1667045E-03 2.7595520E-02 at 180iterations finished qdiffx linear iterations at : 14:06:46 total time elapsed so far: 15.05000 # loops : 180 mean,max change (kT/e) : 1.1667045E-03 2.7595520E-02 energy calculations done at 15.05000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.23000 DelPhi exited at 14:06:46 15.232u 0.255s 0:15.76 98.2% 0+0k 0+0io 0pf+0w