Tue Oct 11 07:49:09 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 Tue Oct 11 2011 at 07:49:09 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: 336 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2763 !!! WARNING: HIQ 55 has a net charge of 0.5140 !!! WARNING: GLM 204 has a net charge of -0.0940 !!! WARNING: SEP 207 has a net charge of -0.4750 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: 0.6344228 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): -13.54100 42.57300 ymin,ymax (A): -21.71000 28.57700 zmin,zma (A): -11.63400 40.51300 x,y,z range (A): 56.11400 50.28700 52.14700 scale (grids/A): 0.6344228 object centre (A): 14.51600 3.433499 14.43950 number of atom coordinates read : 2763 total number of charged atoms : 2394 net assigned charge : 9.945019 assigned positive charge : 387.1711 centred at (gu) : 90.05073 87.66996 90.84491 assigned negative charge : -377.2267 centred at (gu) : 90.02562 87.62534 91.07287 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6710 nv = 96 ne = 84 npr = 51553 no. pairs analyzed = 51553 no. exposed pairs = 2990 no. arc points = 20650 no. surface atoms = 1017 nbur = 1746 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 326 mr = 3794 m= 2 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 3202 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2103 ## 247 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 8122 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.8407293E-08 -1.2185851E-08 midg,1,midg; midg,igrid,midg 1.3316484E-08 1.0380689E-08 1,midg,midg; igrid,midg,midg 1.0050258E-08 1.5164080E-08 gauss-seidel spectral radius is 0.9871165 estimated iterations to convergence 72 setup time was (sec) 0.3900000 now iterating at: 07:49:10 rms-change max change #iterations 0.1455132 18.97903 at 10iterations 1.4784881E-02 2.166138 at 20iterations 1.7355822E-03 0.2455826 at 30iterations 2.8452833E-04 4.8393250E-02 at 40iterations 6.0343034E-05 9.2391968E-03 at 50iterations finished qdiffx linear iterations at : 07:49:13 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 6.0343034E-05 9.2391968E-03 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 07:49:13 3.409u 0.229s 0:03.98 90.9% 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 Tue Oct 11 2011 at 07:49:13 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: 336 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2763 !!! WARNING: HIQ 55 has a net charge of 0.5140 !!! WARNING: GLM 204 has a net charge of -0.0940 !!! WARNING: SEP 207 has a net charge of -0.4750 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: 1.903268 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): -13.54100 42.57300 ymin,ymax (A): -21.71000 28.57700 zmin,zma (A): -11.63400 40.51300 x,y,z range (A): 56.11400 50.28700 52.14700 scale (grids/A): 1.903268 object centre (A): 14.51600 3.433499 14.43950 number of atom coordinates read : 2763 total number of charged atoms : 2394 net assigned charge : 9.945019 assigned positive charge : 387.1711 centred at (gu) : 90.15171 83.00947 92.53423 assigned negative charge : -377.2267 centred at (gu) : 90.07669 82.87583 93.21857 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 72081 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20650 grid for indexing accessible points = 1.400000 m= 26309 mr = 50849 m= 3924 mr = 19838 m= 223 mr = 2485 m= 4 mr = 75 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 757 time to turn everything in is 0.3600000 number of dielectric boundary points 29294 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 198 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 18823 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) : 0.6344228 object centre at (A) : 14.51600 3.433499 14.43950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.5594653E-02 -1.3300803E-02 midg,1,midg; midg,igrid,midg 1.4136370E-02 2.3753667E-02 1,midg,midg; igrid,midg,midg 2.1728689E-02 4.5374501E-02 gauss-seidel spectral radius is 0.9986160 estimated iterations to convergence 213 setup time was (sec) 0.5700000 now iterating at: 07:49:14 rms-change max change #iterations 4.170237 188.0905 at 10iterations 1.946680 63.88811 at 20iterations 0.9084784 29.60773 at 30iterations 0.4247038 13.77694 at 40iterations 0.1989633 6.264664 at 50iterations 9.2811823E-02 2.941001 at 60iterations 4.3445177E-02 1.452690 at 70iterations 2.0327754E-02 0.6453772 at 80iterations 9.6056210E-03 0.3091669 at 90iterations 4.5274850E-03 0.1521084 at 100iterations 2.1510599E-03 7.5454712E-02 at 110iterations 1.0459910E-03 3.6701202E-02 at 120iterations finished qdiffx linear iterations at : 07:49:21 total time elapsed so far: 7.640000 # loops : 120 mean,max change (kT/e) : 1.0459910E-03 3.6701202E-02 energy calculations done at 7.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.770000 DelPhi exited at 07:49:22 7.776u 0.230s 0:08.44 94.7% 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 Tue Oct 11 2011 at 07:49:22 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: 336 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2763 !!! WARNING: HIQ 55 has a net charge of 0.5140 !!! WARNING: GLM 204 has a net charge of -0.0940 !!! WARNING: SEP 207 has a net charge of -0.4750 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: 2.854903 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): -13.54100 42.57300 ymin,ymax (A): -21.71000 28.57700 zmin,zma (A): -11.63400 40.51300 x,y,z range (A): 56.11400 50.28700 52.14700 scale (grids/A): 2.854903 object centre (A): 14.51600 3.433499 14.43950 number of atom coordinates read : 2763 total number of charged atoms : 2394 net assigned charge : 9.945019 assigned positive charge : 387.1711 centred at (gu) : 90.22747 79.51415 93.80124 assigned negative charge : -377.2267 centred at (gu) : 90.11501 79.31367 94.82780 start vw surface at 0.1000000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 166622 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20650 grid for indexing accessible points = 1.400000 m= 85401 mr = 122657 m= 30501 mr = 71189 m= 6980 mr = 24693 m= 1010 mr = 5265 m= 50 mr = 695 m= 0 mr = 15 time to grow re-entrant surface = 0.5400000 no. cavity mid-points inaccessible to solvent = 2481 time to turn everything in is 0.9600000 number of dielectric boundary points 66050 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.040000 number of grid points assigned charge 19140 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) : 1.903268 object centre at (A) : 14.51600 3.433499 14.43950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.7316154 -0.2343301 midg,1,midg; midg,igrid,midg 0.1437540 0.2703940 1,midg,midg; igrid,midg,midg 0.1241747 0.3680154 gauss-seidel spectral radius is 0.9992424 estimated iterations to convergence 287 setup time was (sec) 1.190000 now iterating at: 07:49:23 rms-change max change #iterations 9.698845 424.3824 at 10iterations 5.601866 137.6977 at 20iterations 3.219207 77.98820 at 30iterations 1.850870 44.16108 at 40iterations 1.061109 19.78115 at 50iterations 0.6081914 11.77851 at 60iterations 0.3477056 6.387344 at 70iterations 0.1990431 3.738987 at 80iterations 0.1136498 2.103725 at 90iterations 6.5063484E-02 1.161335 at 100iterations 3.7159234E-02 0.7014542 at 110iterations 2.1369375E-02 0.3892288 at 120iterations 1.2247244E-02 0.2301998 at 130iterations 7.0529291E-03 0.1378174 at 140iterations 4.0933359E-03 8.4476471E-02 at 150iterations 2.4100824E-03 4.8488617E-02 at 160iterations 1.4500616E-03 3.0870438E-02 at 170iterations 9.0156135E-04 1.7471313E-02 at 180iterations finished qdiffx linear iterations at : 07:49:35 total time elapsed so far: 12.59000 # loops : 180 mean,max change (kT/e) : 9.0156135E-04 1.7471313E-02 energy calculations done at 12.59000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.73000 DelPhi exited at 07:49:35 12.729u 0.223s 0:13.65 94.7% 0+0k 0+0io 0pf+0w