Mon Oct 10 17:01:24 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 17:01:24 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 = 2950 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6303228 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): -8.899000 47.58000 ymin,ymax (A): -6.903000 42.18600 zmin,zma (A): 0.8850001 55.45500 x,y,z range (A): 56.47900 49.08900 54.57000 scale (grids/A): 0.6303228 object centre (A): 19.34050 17.64150 28.17000 number of atom coordinates read : 2950 total number of charged atoms : 2809 net assigned charge : -4.999966 assigned positive charge : 443.0020 centred at (gu) : 89.71263 89.36913 88.59494 assigned negative charge : -448.0032 centred at (gu) : 89.67299 89.27515 88.47830 start vw surface at 0.1600000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7836 nv = 96 ne = 84 npr = 59642 no. pairs analyzed = 59642 no. exposed pairs = 3882 no. arc points = 27219 no. surface atoms = 1303 nbur = 1647 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 382 mr = 4087 m= 0 mr = 41 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 39 time to turn everything in is 0.3200000 number of dielectric boundary points 4090 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2745 ## 211 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 9548 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.3597815E-08 4.8109943E-09 midg,1,midg; midg,igrid,midg -1.7153805E-08 3.7610475E-09 1,midg,midg; igrid,midg,midg -9.8754933E-09 -1.0863143E-09 gauss-seidel spectral radius is 0.9869980 estimated iterations to convergence 72 setup time was (sec) 0.5300000 now iterating at: 17:01:25 rms-change max change #iterations 0.1439868 24.00879 at 10iterations 1.3653422E-02 1.954655 at 20iterations 1.3120730E-03 0.1715031 at 30iterations 1.2321408E-04 1.6540527E-02 at 40iterations 1.2050505E-05 1.6918182E-03 at 50iterations finished qdiffx linear iterations at : 17:01:27 total time elapsed so far: 3.100000 # loops : 50 mean,max change (kT/e) : 1.2050505E-05 1.6918182E-03 energy calculations done at 3.100000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.270000 DelPhi exited at 17:01:28 3.278u 0.164s 0:03.83 89.5% 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 17:01:28 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 = 2950 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.890968 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): -8.899000 47.58000 ymin,ymax (A): -6.903000 42.18600 zmin,zma (A): 0.8850001 55.45500 x,y,z range (A): 56.47900 49.08900 54.57000 scale (grids/A): 1.890968 object centre (A): 19.34050 17.64150 28.17000 number of atom coordinates read : 2950 total number of charged atoms : 2809 net assigned charge : -4.999966 assigned positive charge : 443.0020 centred at (gu) : 89.13670 88.10672 85.78378 assigned negative charge : -448.0032 centred at (gu) : 89.01890 87.82514 85.43475 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 84342 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27219 grid for indexing accessible points = 1.400000 m= 28812 mr = 56858 m= 4126 mr = 20420 m= 214 mr = 2394 m= 2 mr = 59 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 1120 time to turn everything in is 0.5700000 number of dielectric boundary points 37765 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 175 iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 22084 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) : 0.6303228 object centre at (A) : 19.34050 17.64150 28.17000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.6556536E-03 1.5232404E-02 midg,1,midg; midg,igrid,midg -2.9409697E-02 6.5186853E-04 1,midg,midg; igrid,midg,midg -5.9993353E-02 1.5021523E-02 gauss-seidel spectral radius is 0.9986535 estimated iterations to convergence 216 setup time was (sec) 0.8300000 now iterating at: 17:01:29 rms-change max change #iterations 4.509178 182.4118 at 10iterations 2.116445 74.08211 at 20iterations 0.9946980 33.32412 at 30iterations 0.4666854 15.11346 at 40iterations 0.2194482 6.542679 at 50iterations 0.1030286 3.253357 at 60iterations 4.8555385E-02 1.348083 at 70iterations 2.2765649E-02 0.6893272 at 80iterations 1.0710026E-02 0.3078589 at 90iterations 5.0290939E-03 0.1462269 at 100iterations 2.3776593E-03 7.2956085E-02 at 110iterations 1.1160747E-03 3.4662247E-02 at 120iterations finished qdiffx linear iterations at : 17:01:35 total time elapsed so far: 7.010000 # loops : 120 mean,max change (kT/e) : 1.1160747E-03 3.4662247E-02 energy calculations done at 7.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.180000 DelPhi exited at 17:01:36 7.183u 0.182s 0:08.71 84.5% 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 17:01:37 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 = 2950 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.836452 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): -8.899000 47.58000 ymin,ymax (A): -6.903000 42.18600 zmin,zma (A): 0.8850001 55.45500 x,y,z range (A): 56.47900 49.08900 54.57000 scale (grids/A): 2.836452 object centre (A): 19.34050 17.64150 28.17000 number of atom coordinates read : 2950 total number of charged atoms : 2809 net assigned charge : -4.999966 assigned positive charge : 443.0020 centred at (gu) : 88.70498 87.15981 83.67548 assigned negative charge : -448.0032 centred at (gu) : 88.52824 86.73766 83.15215 start vw surface at 0.1700000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 195389 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27219 grid for indexing accessible points = 1.400000 m= 94344 mr = 138799 m= 32285 mr = 75137 m= 7224 mr = 25285 m= 884 mr = 5135 m= 48 mr = 556 m= 0 mr = 20 time to grow re-entrant surface = 0.8300000 no. cavity mid-points inaccessible to solvent = 3566 time to turn everything in is 1.440000 number of dielectric boundary points 85242 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.570000 number of grid points assigned charge 22471 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) : 1.890968 object centre at (A) : 19.34050 17.64150 28.17000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2960545 0.1147638 midg,1,midg; midg,igrid,midg -0.2672229 3.2009181E-02 1,midg,midg; igrid,midg,midg -0.7301893 0.3199517 gauss-seidel spectral radius is 0.9992882 estimated iterations to convergence 296 setup time was (sec) 1.720000 now iterating at: 17:01:39 rms-change max change #iterations 10.88467 387.9551 at 10iterations 6.526502 150.3424 at 20iterations 3.870366 89.29910 at 30iterations 2.285979 50.58089 at 40iterations 1.344642 28.33766 at 50iterations 0.7877325 17.55684 at 60iterations 0.4609737 8.544985 at 70iterations 0.2694149 4.547985 at 80iterations 0.1572689 2.896574 at 90iterations 9.1553852E-02 1.601776 at 100iterations 5.3393688E-02 0.9045305 at 110iterations 3.1032071E-02 0.5532537 at 120iterations 1.8084018E-02 0.3217773 at 130iterations 1.0503383E-02 0.1926136 at 140iterations 6.1008297E-03 0.1041241 at 150iterations 3.5475721E-03 5.8578432E-02 at 160iterations 2.0627109E-03 3.9367676E-02 at 170iterations 1.1994560E-03 2.0935059E-02 at 180iterations finished qdiffx linear iterations at : 17:01:48 total time elapsed so far: 11.22000 # loops : 180 mean,max change (kT/e) : 1.1994560E-03 2.0935059E-02 energy calculations done at 11.22000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.42000 DelPhi exited at 17:01:52 11.418u 0.220s 0:14.90 78.0% 0+0k 0+0io 0pf+0w