Mon Oct 10 14:04:04 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 14:04:04 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: 315 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2878 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: 0.6003271 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): -10.32600 37.36200 ymin,ymax (A): 9.7000003E-02 59.39800 zmin,zma (A): -24.04700 27.93800 x,y,z range (A): 47.68800 59.30100 51.98500 scale (grids/A): 0.6003271 object centre (A): 13.51800 29.74750 1.945500 number of atom coordinates read : 2878 total number of charged atoms : 2499 net assigned charge : 9.500011 assigned positive charge : 390.8412 centred at (gu) : 90.01293 88.78318 89.78131 assigned negative charge : -381.3426 centred at (gu) : 90.10414 88.71373 89.83502 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6514 nv = 96 ne = 84 npr = 51174 no. pairs analyzed = 51174 no. exposed pairs = 3674 no. arc points = 25759 no. surface atoms = 1214 nbur = 1664 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 305 mr = 3294 m= 2 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 13 time to turn everything in is 0.1900000 number of dielectric boundary points 3506 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2512 ## 256 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 7901 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.3760450E-09 2.0885083E-09 midg,1,midg; midg,igrid,midg 2.0564668E-09 5.0616151E-09 1,midg,midg; igrid,midg,midg 7.3842390E-09 8.0857349E-10 gauss-seidel spectral radius is 0.9856511 estimated iterations to convergence 68 setup time was (sec) 0.3800000 now iterating at: 14:04:05 rms-change max change #iterations 0.1084784 16.89772 at 10iterations 9.2315516E-03 1.396416 at 20iterations 8.1865408E-04 0.1118851 at 30iterations 1.2718083E-04 2.0174026E-02 at 40iterations 4.7544592E-05 7.3881149E-03 at 50iterations finished qdiffx linear iterations at : 14:04:08 total time elapsed so far: 3.190000 # loops : 50 mean,max change (kT/e) : 4.7544592E-05 7.3881149E-03 energy calculations done at 3.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.350000 DelPhi exited at 14:04:08 3.354u 0.170s 0:04.21 83.6% 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 14:04:09 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: 315 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2878 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: 1.800981 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): -10.32600 37.36200 ymin,ymax (A): 9.7000003E-02 59.39800 zmin,zma (A): -24.04700 27.93800 x,y,z range (A): 47.68800 59.30100 51.98500 scale (grids/A): 1.800981 object centre (A): 13.51800 29.74750 1.945500 number of atom coordinates read : 2878 total number of charged atoms : 2499 net assigned charge : 9.500011 assigned positive charge : 390.8412 centred at (gu) : 90.03792 86.34897 89.34325 assigned negative charge : -381.3426 centred at (gu) : 90.31214 86.14082 89.50475 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 70556 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25759 grid for indexing accessible points = 1.400000 m= 24106 mr = 47097 m= 3326 mr = 16800 m= 134 mr = 1821 m= 1 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 1376 time to turn everything in is 0.3500000 number of dielectric boundary points 32371 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 165 iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 19333 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) : 0.6003271 object centre at (A) : 13.51800 29.74750 1.945500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.7871588E-02 -3.8492882E-03 midg,1,midg; midg,igrid,midg -1.3739969E-04 1.8293560E-02 1,midg,midg; igrid,midg,midg 2.2169266E-02 4.3496909E-03 gauss-seidel spectral radius is 0.9984971 estimated iterations to convergence 205 setup time was (sec) 0.5600000 now iterating at: 14:04:09 rms-change max change #iterations 3.816634 209.3641 at 10iterations 1.724088 64.46748 at 20iterations 0.7779073 27.08852 at 30iterations 0.3513838 11.96896 at 40iterations 0.1585525 5.476835 at 50iterations 7.1860559E-02 2.364146 at 60iterations 3.2524418E-02 1.163863 at 70iterations 1.4639473E-02 0.4950047 at 80iterations 6.6034254E-03 0.2685585 at 90iterations 2.9938633E-03 0.1010294 at 100iterations 1.3522577E-03 4.9301267E-02 at 110iterations 6.1410671E-04 2.0247459E-02 at 120iterations finished qdiffx linear iterations at : 14:04:16 total time elapsed so far: 7.490000 # loops : 120 mean,max change (kT/e) : 6.1410671E-04 2.0247459E-02 energy calculations done at 7.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.610000 DelPhi exited at 14:04:17 7.617u 0.189s 0:08.29 93.9% 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 Mon Oct 10 2011 at 14:04:17 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: 315 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2878 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: 2.701472 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): -10.32600 37.36200 ymin,ymax (A): 9.7000003E-02 59.39800 zmin,zma (A): -24.04700 27.93800 x,y,z range (A): 47.68800 59.30100 51.98500 scale (grids/A): 2.701472 object centre (A): 13.51800 29.74750 1.945500 number of atom coordinates read : 2878 total number of charged atoms : 2499 net assigned charge : 9.500011 assigned positive charge : 390.8412 centred at (gu) : 90.05660 84.52320 89.01450 assigned negative charge : -381.3426 centred at (gu) : 90.46809 84.21118 89.25723 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 163099 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25759 grid for indexing accessible points = 1.400000 m= 79026 mr = 115011 m= 26796 mr = 62400 m= 5646 mr = 20560 m= 557 mr = 3889 m= 25 mr = 309 m= 0 mr = 2 time to grow re-entrant surface = 0.4900000 no. cavity mid-points inaccessible to solvent = 4776 time to turn everything in is 0.8900000 number of dielectric boundary points 72978 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 0.9900000 number of grid points assigned charge 19960 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) : 1.800981 object centre at (A) : 13.51800 29.74750 1.945500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4067079 -7.4246572E-03 midg,1,midg; midg,igrid,midg -0.1270195 0.1427194 1,midg,midg; igrid,midg,midg 0.2305609 5.1484898E-02 gauss-seidel spectral radius is 0.9992313 estimated iterations to convergence 285 setup time was (sec) 1.130000 now iterating at: 14:04:18 rms-change max change #iterations 9.236979 326.4547 at 10iterations 5.382512 142.9019 at 20iterations 3.113773 69.23729 at 30iterations 1.795495 41.68864 at 40iterations 1.031564 21.17204 at 50iterations 0.5923145 11.36835 at 60iterations 0.3380727 7.108158 at 70iterations 0.1930060 3.730068 at 80iterations 0.1102456 2.161065 at 90iterations 6.2862895E-02 1.211687 at 100iterations 3.5892036E-02 0.7135155 at 110iterations 2.0405274E-02 0.4029555 at 120iterations 1.1670279E-02 0.2135410 at 130iterations 6.6397963E-03 0.1315994 at 140iterations 3.7689188E-03 7.8735352E-02 at 150iterations 2.1465574E-03 4.1824341E-02 at 160iterations 1.2235463E-03 2.2884369E-02 at 170iterations 6.9876079E-04 1.2977600E-02 at 180iterations finished qdiffx linear iterations at : 14:04:29 total time elapsed so far: 12.22000 # loops : 180 mean,max change (kT/e) : 6.9876079E-04 1.2977600E-02 energy calculations done at 12.22000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.34000 DelPhi exited at 14:04:30 12.347u 0.190s 0:12.85 97.5% 0+0k 0+0io 0pf+0w