Mon Oct 10 10:24:38 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 Mon Oct 10 2011 at 10:24:38 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: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2840 !!! WARNING: HIT 231 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5509897 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): 16.55300 81.16400 ymin,ymax (A): 30.93700 88.78100 zmin,zma (A): -1.718000 50.06000 x,y,z range (A): 64.61100 57.84399 51.77800 scale (grids/A): 0.5509897 object centre (A): 48.85850 59.85900 24.17100 number of atom coordinates read : 2840 total number of charged atoms : 2690 net assigned charge : 7.014023 assigned positive charge : 418.9768 centred at (gu) : 88.24374 88.89537 87.07046 assigned negative charge : -411.9633 centred at (gu) : 88.14473 88.84830 86.94161 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 5790 nv = 96 ne = 84 npr = 55095 no. pairs analyzed = 55095 no. exposed pairs = 4161 no. arc points = 29778 no. surface atoms = 1377 nbur = 1463 mkacc time = 0.1300000 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 = 1.540000 m= 257 mr = 2617 m= 1 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 3420 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2888 ## 334 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 7371 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.4093355E-10 7.3767803E-10 midg,1,midg; midg,igrid,midg 2.9158542E-10 6.9930944E-10 1,midg,midg; igrid,midg,midg -2.6195404E-10 8.3915452E-10 gauss-seidel spectral radius is 0.9830176 estimated iterations to convergence 63 setup time was (sec) 0.5900000 now iterating at: 10:24:39 rms-change max change #iterations 7.4800760E-02 13.10616 at 10iterations 5.0525432E-03 0.8724785 at 20iterations 3.6934012E-04 6.6152573E-02 at 30iterations 3.0998570E-05 4.5824051E-03 at 40iterations 4.4083317E-06 4.5824051E-04 at 50iterations finished qdiffx linear iterations at : 10:24:42 total time elapsed so far: 3.500000 # loops : 50 mean,max change (kT/e) : 4.4083317E-06 4.5824051E-04 energy calculations done at 3.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.670000 DelPhi exited at 10:24:42 3.676u 0.288s 0:04.31 91.6% 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 Mon Oct 10 2011 at 10:24:42 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: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2840 !!! WARNING: HIT 231 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.652969 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): 16.55300 81.16400 ymin,ymax (A): 30.93700 88.78100 zmin,zma (A): -1.718000 50.06000 x,y,z range (A): 64.61100 57.84399 51.77800 scale (grids/A): 1.652969 object centre (A): 48.85850 59.85900 24.17100 number of atom coordinates read : 2840 total number of charged atoms : 2690 net assigned charge : 7.014023 assigned positive charge : 418.9768 centred at (gu) : 84.73019 86.68573 81.21109 assigned negative charge : -411.9633 centred at (gu) : 84.43393 86.54459 80.82431 start vw surface at 0.1600000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 63075 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29778 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 18682 mr = 39442 m= 1973 mr = 11755 m= 59 mr = 808 m= 0 mr = 8 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5200000 number of dielectric boundary points 31776 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 279 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 20691 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) : 0.5509897 object centre at (A) : 48.85850 59.85900 24.17100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.2144989E-04 6.2146252E-03 midg,1,midg; midg,igrid,midg 5.0117392E-03 1.4499670E-02 1,midg,midg; igrid,midg,midg -1.4527240E-02 -7.5135627E-03 gauss-seidel spectral radius is 0.9982253 estimated iterations to convergence 189 setup time was (sec) 0.8800000 now iterating at: 10:24:44 rms-change max change #iterations 3.306499 175.9327 at 10iterations 1.380670 52.34243 at 20iterations 0.5786489 20.74466 at 30iterations 0.2429220 9.467881 at 40iterations 0.1021228 3.745201 at 50iterations 4.2655893E-02 1.576359 at 60iterations 1.8012533E-02 0.6319427 at 70iterations 7.5285579E-03 0.2814760 at 80iterations 3.1662390E-03 0.1204839 at 90iterations 1.3314583E-03 4.6484470E-02 at 100iterations 5.6182180E-04 2.1309316E-02 at 110iterations 2.3642821E-04 9.3383789E-03 at 120iterations finished qdiffx linear iterations at : 10:24:51 total time elapsed so far: 7.980000 # loops : 120 mean,max change (kT/e) : 2.3642821E-04 9.3383789E-03 energy calculations done at 7.980000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.180000 DelPhi exited at 10:24:52 8.185u 0.258s 0:09.09 92.7% 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 10:24:52 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: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2840 !!! WARNING: HIT 231 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.479454 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): 16.55300 81.16400 ymin,ymax (A): 30.93700 88.78100 zmin,zma (A): -1.718000 50.06000 x,y,z range (A): 64.61100 57.84399 51.77800 scale (grids/A): 2.479454 object centre (A): 48.85850 59.85900 24.17100 number of atom coordinates read : 2840 total number of charged atoms : 2690 net assigned charge : 7.014023 assigned positive charge : 418.9768 centred at (gu) : 82.09506 85.02840 76.81654 assigned negative charge : -411.9633 centred at (gu) : 81.65074 84.81685 76.23643 start vw surface at 0.1500000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 146224 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29778 grid for indexing accessible points = 1.400000 m= 63786 mr = 97513 m= 18265 mr = 47708 m= 2751 mr = 12658 m= 190 mr = 1558 m= 6 mr = 68 m= 0 mr = 1 time to grow re-entrant surface = 0.6700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.190000 number of dielectric boundary points 71716 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 25 iepsmp to db, and charging done at 1.350000 number of grid points assigned charge 21507 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) : 1.652969 object centre at (A) : 48.85850 59.85900 24.17100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.1023184E-02 6.6407919E-02 midg,1,midg; midg,igrid,midg -5.0448984E-02 0.3114443 1,midg,midg; igrid,midg,midg -0.5278542 -0.3302274 gauss-seidel spectral radius is 0.9991527 estimated iterations to convergence 271 setup time was (sec) 1.550000 now iterating at: 10:24:53 rms-change max change #iterations 8.748957 292.3711 at 10iterations 5.043312 141.3474 at 20iterations 2.884113 80.92369 at 30iterations 1.629681 43.71177 at 40iterations 0.9148449 28.50340 at 50iterations 0.5127366 14.51341 at 60iterations 0.2862002 7.311681 at 70iterations 0.1593599 3.452649 at 80iterations 8.8350981E-02 2.075385 at 90iterations 4.9003311E-02 1.242871 at 100iterations 2.7204173E-02 0.6322851 at 110iterations 1.5037727E-02 0.3582239 at 120iterations 8.3300341E-03 0.1830551 at 130iterations 4.6180752E-03 0.1036758 at 140iterations 2.5439798E-03 5.5844545E-02 at 150iterations 1.4081898E-03 3.1757355E-02 at 160iterations 7.7826431E-04 1.8582821E-02 at 170iterations 4.3063494E-04 9.8304749E-03 at 180iterations finished qdiffx linear iterations at : 10:25:05 total time elapsed so far: 13.23000 # loops : 180 mean,max change (kT/e) : 4.3063494E-04 9.8304749E-03 energy calculations done at 13.23000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.42000 DelPhi exited at 10:25:06 13.418u 0.224s 0:14.28 95.4% 0+0k 0+0io 0pf+0w