Sat Oct 15 14:35:38 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+sph2.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 = amb2.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 Sat Oct 15 2011 at 14:35:39 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: 285 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2782 !!! WARNING: HIT 107 has a net charge of 0.5140 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: 0.6152145 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): -9.238000 48.62800 ymin,ymax (A): -8.106000 38.75900 zmin,zma (A): 1.683000 56.93200 x,y,z range (A): 57.86600 46.86500 55.24900 scale (grids/A): 0.6152145 object centre (A): 19.69500 15.32650 29.30750 number of atom coordinates read : 2782 total number of charged atoms : 2641 net assigned charge : -0.9859689 assigned positive charge : 420.9123 centred at (gu) : 89.02167 89.77169 88.30692 assigned negative charge : -421.8993 centred at (gu) : 88.92713 89.69685 88.29472 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7135 nv = 96 ne = 84 npr = 54996 no. pairs analyzed = 54996 no. exposed pairs = 3778 no. arc points = 26676 no. surface atoms = 1269 nbur = 1513 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 347 mr = 3619 m= 2 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 15 time to turn everything in is 0.2000000 number of dielectric boundary points 3839 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2701 ## 263 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 8692 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.9682933E-09 1.1099897E-10 midg,1,midg; midg,igrid,midg -5.5871454E-09 3.8499688E-09 1,midg,midg; igrid,midg,midg -8.1898470E-09 4.2189439E-09 gauss-seidel spectral radius is 0.9863447 estimated iterations to convergence 70 setup time was (sec) 0.4000000 now iterating at: 14:35:39 rms-change max change #iterations 0.1256500 20.28433 at 10iterations 1.1241964E-02 1.877855 at 20iterations 1.0281259E-03 0.1347427 at 30iterations 9.8372868E-05 1.5026093E-02 at 40iterations 1.1941377E-05 1.9607544E-03 at 50iterations finished qdiffx linear iterations at : 14:35:43 total time elapsed so far: 3.480000 # loops : 50 mean,max change (kT/e) : 1.1941377E-05 1.9607544E-03 energy calculations done at 3.480000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.620000 DelPhi exited at 14:35:44 3.621u 0.230s 0:05.33 72.2% 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 Sat Oct 15 2011 at 14:35:44 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: 285 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2782 !!! WARNING: HIT 107 has a net charge of 0.5140 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: 1.845643 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): -9.238000 48.62800 ymin,ymax (A): -8.106000 38.75900 zmin,zma (A): 1.683000 56.93200 x,y,z range (A): 57.86600 46.86500 55.24900 scale (grids/A): 1.845643 object centre (A): 19.69500 15.32650 29.30750 number of atom coordinates read : 2782 total number of charged atoms : 2641 net assigned charge : -0.9859689 assigned positive charge : 420.9123 centred at (gu) : 87.06409 89.31440 84.91992 assigned negative charge : -421.8993 centred at (gu) : 86.78098 89.09040 84.88390 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 77395 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26676 grid for indexing accessible points = 1.400000 m= 25874 mr = 51748 m= 3582 mr = 17853 m= 186 mr = 2021 m= 1 mr = 51 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 447 time to turn everything in is 0.3700000 number of dielectric boundary points 35365 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 183 iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 20682 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) : 0.6152145 object centre at (A) : 19.69500 15.32650 29.30750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.8199925E-03 1.5590455E-02 midg,1,midg; midg,igrid,midg -1.7609516E-02 7.2802044E-03 1,midg,midg; igrid,midg,midg -4.7783639E-02 2.4109753E-02 gauss-seidel spectral radius is 0.9985756 estimated iterations to convergence 210 setup time was (sec) 0.6100000 now iterating at: 14:35:45 rms-change max change #iterations 4.184848 187.9702 at 10iterations 1.920338 71.02092 at 20iterations 0.8785146 30.08308 at 30iterations 0.4043656 13.24059 at 40iterations 0.1854879 5.720459 at 50iterations 8.5273057E-02 3.030823 at 60iterations 3.9276931E-02 1.253269 at 70iterations 1.8023295E-02 0.5264702 at 80iterations 8.2949344E-03 0.2530289 at 90iterations 3.8185597E-03 0.1239510 at 100iterations 1.7655760E-03 5.4664612E-02 at 110iterations 8.1271504E-04 2.5881201E-02 at 120iterations finished qdiffx linear iterations at : 14:35:57 total time elapsed so far: 8.270000 # loops : 120 mean,max change (kT/e) : 8.1271504E-04 2.5881201E-02 energy calculations done at 8.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.410000 DelPhi exited at 14:35:58 8.414u 0.223s 0:13.64 63.2% 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 Sat Oct 15 2011 at 14:35:58 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: 285 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2782 !!! WARNING: HIT 107 has a net charge of 0.5140 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: 2.768465 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): -9.238000 48.62800 ymin,ymax (A): -8.106000 38.75900 zmin,zma (A): 1.683000 56.93200 x,y,z range (A): 57.86600 46.86500 55.24900 scale (grids/A): 2.768465 object centre (A): 19.69500 15.32650 29.30750 number of atom coordinates read : 2782 total number of charged atoms : 2641 net assigned charge : -0.9859689 assigned positive charge : 420.9123 centred at (gu) : 85.59597 88.97135 82.37981 assigned negative charge : -421.8993 centred at (gu) : 85.17146 88.63549 82.32576 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 179494 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26676 grid for indexing accessible points = 1.400000 m= 85538 mr = 126637 m= 28376 mr = 67578 m= 6110 mr = 21651 m= 750 mr = 4255 m= 28 mr = 434 m= 0 mr = 7 time to grow re-entrant surface = 0.5700001 no. cavity mid-points inaccessible to solvent = 1441 time to turn everything in is 1.020000 number of dielectric boundary points 79734 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.130000 number of grid points assigned charge 21127 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) : 1.845643 object centre at (A) : 19.69500 15.32650 29.30750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1534191 0.2933692 midg,1,midg; midg,igrid,midg -0.1354526 7.2209790E-02 1,midg,midg; igrid,midg,midg -0.6721500 0.2842513 gauss-seidel spectral radius is 0.9992639 estimated iterations to convergence 291 setup time was (sec) 1.280000 now iterating at: 14:36:00 rms-change max change #iterations 10.27836 387.9553 at 10iterations 6.131093 152.8208 at 20iterations 3.614722 82.68153 at 30iterations 2.113229 48.61386 at 40iterations 1.230242 23.54623 at 50iterations 0.7164894 15.60842 at 60iterations 0.4154068 9.125442 at 70iterations 0.2401719 5.119743 at 80iterations 0.1390024 2.580888 at 90iterations 8.0117092E-02 1.589365 at 100iterations 4.6306022E-02 0.7842007 at 110iterations 2.6713520E-02 0.5244579 at 120iterations 1.5368305E-02 0.2858849 at 130iterations 8.8570938E-03 0.1676826 at 140iterations 5.0984151E-03 8.9004517E-02 at 150iterations 2.9462394E-03 5.2780151E-02 at 160iterations 1.6982078E-03 3.0780792E-02 at 170iterations 9.7953796E-04 1.8383503E-02 at 180iterations finished qdiffx linear iterations at : 14:36:29 total time elapsed so far: 13.93000 # loops : 180 mean,max change (kT/e) : 9.7953796E-04 1.8383503E-02 energy calculations done at 13.93000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.07000 DelPhi exited at 14:36:30 14.076u 0.277s 0:31.08 46.1% 0+0k 0+0io 0pf+0w