Mon Oct 10 14:40:18 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 Mon Oct 10 2011 at 14:40:19 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2729 !!! WARNING: ADP 662 has a net charge of -2.0000 !!! WARNING: MG6 664 has a net charge of 1.4000 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: 0.5831381 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): -8.243999 52.80500 ymin,ymax (A): -16.09000 34.27800 zmin,zma (A): 77.64799 130.2890 x,y,z range (A): 61.04900 50.36800 52.64101 scale (grids/A): 0.5831381 object centre (A): 22.28050 9.094000 103.9685 number of atom coordinates read : 2729 total number of charged atoms : 2587 net assigned charge : -1.599990 assigned positive charge : 424.7655 centred at (gu) : 92.29344 89.81194 89.38165 assigned negative charge : -426.3664 centred at (gu) : 92.19883 89.91423 89.47173 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 6245 nv = 96 ne = 84 npr = 53042 no. pairs analyzed = 53042 no. exposed pairs = 3771 no. arc points = 26274 no. surface atoms = 1271 nbur = 1458 mkacc time = 9.0000004E-02 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 = 1.484000 m= 312 mr = 3132 m= 1 mr = 27 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 3399 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2702 ## 321 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 7802 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8740598E-09 -2.2314637E-09 midg,1,midg; midg,igrid,midg 1.9798916E-09 -2.7463318E-09 1,midg,midg; igrid,midg,midg -1.5772295E-09 3.0010905E-09 gauss-seidel spectral radius is 0.9848052 estimated iterations to convergence 67 setup time was (sec) 0.3900000 now iterating at: 14:40:19 rms-change max change #iterations 9.7455926E-02 15.35517 at 10iterations 7.7099637E-03 1.128798 at 20iterations 6.8837014E-04 0.1151829 at 30iterations 1.0648958E-04 2.2492409E-02 at 40iterations 2.8101778E-05 6.5107346E-03 at 50iterations finished qdiffx linear iterations at : 14:40:22 total time elapsed so far: 3.310000 # loops : 50 mean,max change (kT/e) : 2.8101778E-05 6.5107346E-03 energy calculations done at 3.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.430000 DelPhi exited at 14:40:22 3.435u 0.188s 0:03.93 91.8% 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 Mon Oct 10 2011 at 14:40:22 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2729 !!! WARNING: ADP 662 has a net charge of -2.0000 !!! WARNING: MG6 664 has a net charge of 1.4000 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: 1.749414 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): -8.243999 52.80500 ymin,ymax (A): -16.09000 34.27800 zmin,zma (A): 77.64799 130.2890 x,y,z range (A): 61.04900 50.36800 52.64101 scale (grids/A): 1.749414 object centre (A): 22.28050 9.094000 103.9685 number of atom coordinates read : 2729 total number of charged atoms : 2587 net assigned charge : -1.599990 assigned positive charge : 424.7655 centred at (gu) : 96.87957 89.43526 88.14455 assigned negative charge : -426.3664 centred at (gu) : 96.59631 89.74240 88.41482 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 67422 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26274 grid for indexing accessible points = 1.400000 m= 22429 mr = 44674 m= 2796 mr = 15074 m= 111 mr = 1373 m= 1 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 31631 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 263 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 20056 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) : 0.5831381 object centre at (A) : 22.28050 9.094000 103.9685 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.1190532E-03 -2.6676793E-02 midg,1,midg; midg,igrid,midg 5.7690833E-03 -1.5012745E-02 1,midg,midg; igrid,midg,midg 1.9101400E-02 4.2179044E-02 gauss-seidel spectral radius is 0.9984121 estimated iterations to convergence 199 setup time was (sec) 0.5600000 now iterating at: 14:40:23 rms-change max change #iterations 3.770036 167.8429 at 10iterations 1.646596 67.94380 at 20iterations 0.7252859 27.11171 at 30iterations 0.3181220 10.37813 at 40iterations 0.1400160 5.154491 at 50iterations 6.1689697E-02 2.161071 at 60iterations 2.7220149E-02 0.9889436 at 70iterations 1.1997824E-02 0.4073200 at 80iterations 5.3110998E-03 0.1932168 at 90iterations 2.3492062E-03 7.7076912E-02 at 100iterations 1.0499593E-03 3.7794113E-02 at 110iterations 4.7199152E-04 1.5901633E-02 at 120iterations finished qdiffx linear iterations at : 14:40:30 total time elapsed so far: 7.690000 # loops : 120 mean,max change (kT/e) : 4.7199152E-04 1.5901633E-02 energy calculations done at 7.690000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.820000 DelPhi exited at 14:40:31 7.819u 0.213s 0:08.33 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 14:40:31 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2729 !!! WARNING: ADP 662 has a net charge of -2.0000 !!! WARNING: MG6 664 has a net charge of 1.4000 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: 2.624122 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): -8.243999 52.80500 ymin,ymax (A): -16.09000 34.27800 zmin,zma (A): 77.64799 130.2890 x,y,z range (A): 61.04900 50.36800 52.64101 scale (grids/A): 2.624122 object centre (A): 22.28050 9.094000 103.9685 number of atom coordinates read : 2729 total number of charged atoms : 2587 net assigned charge : -1.599990 assigned positive charge : 424.7655 centred at (gu) : 100.3192 89.15267 87.21674 assigned negative charge : -426.3664 centred at (gu) : 99.89434 89.61353 87.62220 start vw surface at 0.1000000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 156183 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26274 grid for indexing accessible points = 1.400000 m= 74557 mr = 109661 m= 23970 mr = 57866 m= 4661 mr = 17781 m= 480 mr = 2985 m= 10 mr = 253 m= 0 mr = 0 time to grow re-entrant surface = 0.4900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8500000 number of dielectric boundary points 71315 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.9400000 number of grid points assigned charge 20683 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) : 1.749414 object centre at (A) : 22.28050 9.094000 103.9685 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.0393089E-02 -0.3648455 midg,1,midg; midg,igrid,midg 7.4035197E-02 -0.1467083 1,midg,midg; igrid,midg,midg 0.4756249 0.4778704 gauss-seidel spectral radius is 0.9992054 estimated iterations to convergence 280 setup time was (sec) 1.080000 now iterating at: 14:40:32 rms-change max change #iterations 9.486108 283.2722 at 10iterations 5.495934 125.1984 at 20iterations 3.149535 64.91359 at 30iterations 1.799046 37.41556 at 40iterations 1.022441 20.09541 at 50iterations 0.5802927 12.02006 at 60iterations 0.3286499 6.721599 at 70iterations 0.1859307 3.801796 at 80iterations 0.1050871 2.089409 at 90iterations 5.9226643E-02 1.236963 at 100iterations 3.3477671E-02 0.7671661 at 110iterations 1.8912567E-02 0.3877077 at 120iterations 1.0642655E-02 0.2136898 at 130iterations 6.0085910E-03 0.1247863 at 140iterations 3.3875278E-03 6.9063187E-02 at 150iterations 1.9183842E-03 3.9192200E-02 at 160iterations 1.0919857E-03 2.3290634E-02 at 170iterations 6.2399678E-04 1.1966705E-02 at 180iterations finished qdiffx linear iterations at : 14:40:43 total time elapsed so far: 12.18000 # loops : 180 mean,max change (kT/e) : 6.2399678E-04 1.1966705E-02 energy calculations done at 12.18000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.33000 DelPhi exited at 14:40:44 12.328u 0.195s 0:13.13 95.2% 0+0k 0+0io 0pf+0w