Mon Oct 10 10:31:24 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+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 10:31:24 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: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2832 !!! 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5571554 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): 18.02700 81.92300 ymin,ymax (A): 31.31700 87.46600 zmin,zma (A): -1.676000 50.64900 x,y,z range (A): 63.89600 56.14900 52.32500 scale (grids/A): 0.5571554 object centre (A): 49.97500 59.39150 24.48650 number of atom coordinates read : 2832 total number of charged atoms : 2680 net assigned charge : 4.014019 assigned positive charge : 416.0269 centred at (gu) : 87.70174 89.15172 86.88335 assigned negative charge : -412.0133 centred at (gu) : 87.59250 89.10946 86.76534 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 5914 nv = 96 ne = 84 npr = 55561 no. pairs analyzed = 55561 no. exposed pairs = 4108 no. arc points = 29780 no. surface atoms = 1365 nbur = 1467 mkacc time = 0.1200000 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= 266 mr = 2688 m= 2 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 3485 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2985 ## 347 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 7581 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.4391641E-09 7.1076567E-10 midg,1,midg; midg,igrid,midg 6.8274865E-11 6.7329653E-10 1,midg,midg; igrid,midg,midg -1.0148041E-09 8.1812568E-10 gauss-seidel spectral radius is 0.9833881 estimated iterations to convergence 64 setup time was (sec) 0.5500000 now iterating at: 10:31:25 rms-change max change #iterations 8.0406442E-02 17.26650 at 10iterations 5.5904170E-03 0.9459381 at 20iterations 3.9874410E-04 7.2722435E-02 at 30iterations 3.8197773E-05 5.3219795E-03 at 40iterations 5.9248309E-06 7.6770782E-04 at 50iterations finished qdiffx linear iterations at : 10:31:27 total time elapsed so far: 3.230000 # loops : 50 mean,max change (kT/e) : 5.9248309E-06 7.6770782E-04 energy calculations done at 3.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.400000 DelPhi exited at 10:31:28 3.408u 0.191s 0:03.96 90.6% 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 10:31:28 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: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2832 !!! 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.671466 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): 18.02700 81.92300 ymin,ymax (A): 31.31700 87.46600 zmin,zma (A): -1.676000 50.64900 x,y,z range (A): 63.89600 56.14900 52.32500 scale (grids/A): 1.671466 object centre (A): 49.97500 59.39150 24.48650 number of atom coordinates read : 2832 total number of charged atoms : 2680 net assigned charge : 4.014019 assigned positive charge : 416.0269 centred at (gu) : 83.10464 87.45438 80.64957 assigned negative charge : -412.0133 centred at (gu) : 82.77708 87.32798 80.29550 start vw surface at 0.1600000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 63913 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29780 grid for indexing accessible points = 1.400000 m= 20354 mr = 39904 m= 2434 mr = 13334 m= 62 mr = 1065 m= 0 mr = 6 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4700000 number of dielectric boundary points 32454 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 271 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 20598 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) : 0.5571554 object centre at (A) : 49.97500 59.39150 24.48650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.3030984E-03 4.8863241E-03 midg,1,midg; midg,igrid,midg 5.2087065E-03 1.8183157E-02 1,midg,midg; igrid,midg,midg -2.2843610E-02 -1.0150895E-02 gauss-seidel spectral radius is 0.9982640 estimated iterations to convergence 191 setup time was (sec) 0.7700000 now iterating at: 10:31:29 rms-change max change #iterations 3.360586 157.5048 at 10iterations 1.420920 55.89186 at 20iterations 0.6030554 22.22315 at 30iterations 0.2538733 10.33963 at 40iterations 0.1076889 3.848690 at 50iterations 4.5577805E-02 1.542237 at 60iterations 1.9358521E-02 0.6997643 at 70iterations 8.1981299E-03 0.2839928 at 80iterations 3.4699340E-03 0.1259308 at 90iterations 1.4780638E-03 5.7811737E-02 at 100iterations 6.2843558E-04 2.4204254E-02 at 110iterations 2.6810763E-04 9.5653534E-03 at 120iterations finished qdiffx linear iterations at : 10:31:35 total time elapsed so far: 7.320000 # loops : 120 mean,max change (kT/e) : 2.6810763E-04 9.5653534E-03 energy calculations done at 7.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.510000 DelPhi exited at 10:31:36 7.516u 0.216s 0:08.02 96.2% 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 Mon Oct 10 2011 at 10:31:36 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 = 2832 !!! 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: 2.507199 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): 18.02700 81.92300 ymin,ymax (A): 31.31700 87.46600 zmin,zma (A): -1.676000 50.64900 x,y,z range (A): 63.89600 56.14900 52.32500 scale (grids/A): 2.507199 object centre (A): 49.97500 59.39150 24.48650 number of atom coordinates read : 2832 total number of charged atoms : 2680 net assigned charge : 4.014019 assigned positive charge : 416.0269 centred at (gu) : 79.65683 86.18130 75.97424 assigned negative charge : -412.0133 centred at (gu) : 79.16560 85.99187 75.44312 start vw surface at 0.1500000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 148353 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29780 grid for indexing accessible points = 1.400000 m= 67660 mr = 98839 m= 21087 mr = 51322 m= 3725 mr = 15197 m= 320 mr = 2329 m= 5 mr = 147 m= 0 mr = 0 time to grow re-entrant surface = 0.6100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.070000 number of dielectric boundary points 73316 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 17 iepsmp to db, and charging done at 1.200000 number of grid points assigned charge 21419 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) : 1.671466 object centre at (A) : 49.97500 59.39150 24.48650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.7119912E-03 5.6271538E-02 midg,1,midg; midg,igrid,midg 3.9380576E-02 0.3249900 1,midg,midg; igrid,midg,midg -0.7400022 -0.4289820 gauss-seidel spectral radius is 0.9991659 estimated iterations to convergence 273 setup time was (sec) 1.350000 now iterating at: 10:31:37 rms-change max change #iterations 8.827021 320.8289 at 10iterations 5.091397 132.3698 at 20iterations 2.899438 80.12540 at 30iterations 1.641024 42.75900 at 40iterations 0.9233220 24.84047 at 50iterations 0.5193589 14.87152 at 60iterations 0.2902148 7.373119 at 70iterations 0.1621555 4.104382 at 80iterations 9.0189233E-02 2.366285 at 90iterations 5.0410200E-02 1.102033 at 100iterations 2.7965005E-02 0.6440067 at 110iterations 1.5566288E-02 0.3330636 at 120iterations 8.6513516E-03 0.1916742 at 130iterations 4.8011276E-03 0.1079841 at 140iterations 2.6748485E-03 5.5133820E-02 at 150iterations 1.4847385E-03 3.0518532E-02 at 160iterations 8.2187139E-04 1.9115925E-02 at 170iterations 4.5653191E-04 1.0196686E-02 at 180iterations finished qdiffx linear iterations at : 10:31:47 total time elapsed so far: 11.03000 # loops : 180 mean,max change (kT/e) : 4.5653191E-04 1.0196686E-02 energy calculations done at 11.03000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.21000 DelPhi exited at 10:31:48 11.208u 0.173s 0:11.65 97.5% 0+0k 0+0io 0pf+0w