Sun Oct 9 20:56:23 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 20:56:23 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 = 3163 !!! WARNING: CYS 257 has a net charge of 0.5000 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: 0.6031956 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): -22.12100 31.88200 ymin,ymax (A): -35.76200 23.25700 zmin,zma (A): 10.29600 64.84600 x,y,z range (A): 54.00300 59.01900 54.55000 scale (grids/A): 0.6031956 object centre (A): 4.880500 -6.252499 37.57100 number of atom coordinates read : 3163 total number of charged atoms : 3015 net assigned charge : 5.000019 assigned positive charge : 477.7367 centred at (gu) : 89.42029 92.13583 90.72270 assigned negative charge : -472.7380 centred at (gu) : 89.49391 92.17513 90.78148 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7731 nv = 96 ne = 84 npr = 61945 no. pairs analyzed = 61945 no. exposed pairs = 4202 no. arc points = 30726 no. surface atoms = 1403 nbur = 1760 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 396 mr = 3918 m= 0 mr = 27 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 14 time to turn everything in is 0.3300000 number of dielectric boundary points 4182 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3076 ## 357 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 9681 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.4701007E-09 -5.8502514E-10 midg,1,midg; midg,igrid,midg 2.6933260E-09 6.9955014E-10 1,midg,midg; igrid,midg,midg 6.8036821E-09 -1.0444533E-09 gauss-seidel spectral radius is 0.9858330 estimated iterations to convergence 69 setup time was (sec) 0.5800000 now iterating at: 20:56:23 rms-change max change #iterations 0.1214516 24.23722 at 10iterations 1.0255310E-02 1.386932 at 20iterations 9.0073620E-04 0.1329079 at 30iterations 8.1631319E-05 1.1016846E-02 at 40iterations 9.7302491E-06 1.3084412E-03 at 50iterations finished qdiffx linear iterations at : 20:56:26 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 9.7302491E-06 1.3084412E-03 energy calculations done at 3.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.420000 DelPhi exited at 20:56:26 3.427u 0.207s 0:03.90 92.8% 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 Sun Oct 9 2011 at 20:56:27 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 = 3163 !!! WARNING: CYS 257 has a net charge of 0.5000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.809587 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): -22.12100 31.88200 ymin,ymax (A): -35.76200 23.25700 zmin,zma (A): 10.29600 64.84600 x,y,z range (A): 54.00300 59.01900 54.55000 scale (grids/A): 1.809587 object centre (A): 4.880500 -6.252499 37.57100 number of atom coordinates read : 3163 total number of charged atoms : 3015 net assigned charge : 5.000019 assigned positive charge : 477.7367 centred at (gu) : 88.26034 96.40684 92.16741 assigned negative charge : -472.7380 centred at (gu) : 88.48137 96.52529 92.34387 start vw surface at 0.1600000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 84394 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30726 grid for indexing accessible points = 1.400000 m= 26738 mr = 56051 m= 3557 mr = 18065 m= 172 mr = 1885 m= 0 mr = 48 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 238 time to turn everything in is 0.5700000 number of dielectric boundary points 38812 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 226 iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 23523 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) : 0.6031956 object centre at (A) : 4.880500 -6.252499 37.57100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.3917862E-03 -1.5758360E-02 midg,1,midg; midg,igrid,midg -7.0696854E-04 3.7132703E-02 1,midg,midg; igrid,midg,midg 1.6379910E-02 -1.3435336E-03 gauss-seidel spectral radius is 0.9985639 estimated iterations to convergence 209 setup time was (sec) 0.8700000 now iterating at: 20:56:28 rms-change max change #iterations 4.281847 185.0973 at 10iterations 1.954344 67.83334 at 20iterations 0.8938745 30.95928 at 30iterations 0.4093975 12.92938 at 40iterations 0.1875695 5.409769 at 50iterations 8.5895121E-02 2.598175 at 60iterations 3.9653774E-02 1.179455 at 70iterations 1.8107913E-02 0.5539913 at 80iterations 8.2850028E-03 0.2676048 at 90iterations 3.8063803E-03 0.1114502 at 100iterations 1.7497827E-03 5.5885315E-02 at 110iterations 8.0481777E-04 2.4414539E-02 at 120iterations finished qdiffx linear iterations at : 20:56:34 total time elapsed so far: 7.560000 # loops : 120 mean,max change (kT/e) : 8.0481777E-04 2.4414539E-02 energy calculations done at 7.560000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.720000 DelPhi exited at 20:56:35 7.725u 0.275s 0:08.27 96.6% 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 20:56:35 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 = 3163 !!! WARNING: CYS 257 has a net charge of 0.5000 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: 2.714380 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): -22.12100 31.88200 ymin,ymax (A): -35.76200 23.25700 zmin,zma (A): 10.29600 64.84600 x,y,z range (A): 54.00300 59.01900 54.55000 scale (grids/A): 2.714380 object centre (A): 4.880500 -6.252499 37.57100 number of atom coordinates read : 3163 total number of charged atoms : 3015 net assigned charge : 5.000019 assigned positive charge : 477.7367 centred at (gu) : 87.39016 99.60982 93.25070 assigned negative charge : -472.7380 centred at (gu) : 87.72190 99.78785 93.51575 start vw surface at 0.1600000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 195514 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30726 grid for indexing accessible points = 1.400000 m= 90014 mr = 136979 m= 28302 mr = 70551 m= 6025 mr = 21021 m= 740 mr = 4067 m= 32 mr = 451 m= 0 mr = 11 time to grow re-entrant surface = 0.8200000 no. cavity mid-points inaccessible to solvent = 922 time to turn everything in is 1.430000 number of dielectric boundary points 87547 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 1.590000 number of grid points assigned charge 24118 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) : 1.809587 object centre at (A) : 4.880500 -6.252499 37.57100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1113828 -0.2974896 midg,1,midg; midg,igrid,midg 8.6377859E-02 0.9653305 1,midg,midg; igrid,midg,midg 0.2668806 -6.0911939E-02 gauss-seidel spectral radius is 0.9992651 estimated iterations to convergence 291 setup time was (sec) 1.770000 now iterating at: 20:56:37 rms-change max change #iterations 10.51422 302.4558 at 10iterations 6.274745 163.2476 at 20iterations 3.699098 89.19408 at 30iterations 2.172125 46.23425 at 40iterations 1.267608 25.04968 at 50iterations 0.7385082 15.43511 at 60iterations 0.4294537 7.644120 at 70iterations 0.2495667 4.312992 at 80iterations 0.1444235 2.978881 at 90iterations 8.3638668E-02 1.697056 at 100iterations 4.8265055E-02 0.8305759 at 110iterations 2.7920647E-02 0.5386868 at 120iterations 1.6085867E-02 0.2890854 at 130iterations 9.2983572E-03 0.2382669 at 140iterations 5.3552683E-03 9.6881866E-02 at 150iterations 3.0825899E-03 5.8462143E-02 at 160iterations 1.7810010E-03 3.0539274E-02 at 170iterations 1.0272103E-03 2.1239519E-02 at 180iterations finished qdiffx linear iterations at : 20:56:47 total time elapsed so far: 12.35000 # loops : 180 mean,max change (kT/e) : 1.0272103E-03 2.1239519E-02 energy calculations done at 12.35000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.55000 DelPhi exited at 20:56:48 12.550u 0.253s 0:13.09 97.7% 0+0k 0+0io 0pf+0w