Tue Nov 22 14:12:46 PST 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 Nov 22 2011 at 14:12:50 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: 251 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1958 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: 0.5996193 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): -8.939000 50.43200 ymin,ymax (A): 8.719001 51.55400 zmin,zma (A): -4.035000 38.82300 x,y,z range (A): 59.37100 42.83500 42.85800 scale (grids/A): 0.5996193 object centre (A): 20.74650 30.13650 17.39400 number of atom coordinates read : 1958 total number of charged atoms : 1826 net assigned charge : 5.000012 assigned positive charge : 290.5560 centred at (gu) : 90.17303 89.10406 90.48424 assigned negative charge : -285.5562 centred at (gu) : 90.14986 89.00932 90.62591 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 4756 nv = 96 ne = 84 npr = 39718 no. pairs analyzed = 39718 no. exposed pairs = 2426 no. arc points = 17069 no. surface atoms = 824 nbur = 1134 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 230 mr = 2607 m= 0 mr = 12 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 9 time to turn everything in is 0.2200000 number of dielectric boundary points 2367 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1750 ## 211 charges are in solution ## iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 5786 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.2495075E-09 -1.8656336E-09 midg,1,midg; midg,igrid,midg -4.9173710E-10 3.7997143E-09 1,midg,midg; igrid,midg,midg 1.4908574E-09 2.8844473E-09 gauss-seidel spectral radius is 0.9855524 estimated iterations to convergence 68 setup time was (sec) 0.4400000 now iterating at: 14:12:54 rms-change max change #iterations 9.6437842E-02 17.18849 at 10iterations 8.0431076E-03 1.364662 at 20iterations 6.7618635E-04 0.1409888 at 30iterations 5.5882418E-05 1.1230469E-02 at 40iterations 4.7932531E-06 8.7165833E-04 at 50iterations finished qdiffx linear iterations at : 14:13:01 total time elapsed so far: 2.950000 # loops : 50 mean,max change (kT/e) : 4.7932531E-06 8.7165833E-04 energy calculations done at 2.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.130000 DelPhi exited at 14:13:07 3.135u 0.162s 0:17.34 18.9% 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 Nov 22 2011 at 14:13:09 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: 251 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1958 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: 1.798858 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): -8.939000 50.43200 ymin,ymax (A): 8.719001 51.55400 zmin,zma (A): -4.035000 38.82300 x,y,z range (A): 59.37100 42.83500 42.85800 scale (grids/A): 1.798858 object centre (A): 20.74650 30.13650 17.39400 number of atom coordinates read : 1958 total number of charged atoms : 1826 net assigned charge : 5.000012 assigned positive charge : 290.5560 centred at (gu) : 90.51908 87.31239 91.45279 assigned negative charge : -285.5562 centred at (gu) : 90.44959 87.02811 91.87807 start vw surface at 0.1100000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 51662 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17069 grid for indexing accessible points = 1.400000 m= 17959 mr = 35434 m= 2235 mr = 13371 m= 49 mr = 1297 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 427 time to turn everything in is 0.3700000 number of dielectric boundary points 21798 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 147 iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 14232 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) : 0.5996193 object centre at (A) : 20.74650 30.13650 17.39400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.6844647E-03 -9.9695916E-04 midg,1,midg; midg,igrid,midg 3.6804681E-03 7.1942406E-03 1,midg,midg; igrid,midg,midg 2.6806390E-02 4.0820815E-02 gauss-seidel spectral radius is 0.9983946 estimated iterations to convergence 198 setup time was (sec) 0.6400000 now iterating at: 14:13:13 rms-change max change #iterations 3.194392 138.1755 at 10iterations 1.405212 60.33131 at 20iterations 0.6169291 25.92834 at 30iterations 0.2703397 10.31797 at 40iterations 0.1186036 4.531449 at 50iterations 5.2054442E-02 2.091446 at 60iterations 2.2928316E-02 1.002223 at 70iterations 1.0024895E-02 0.3766251 at 80iterations 4.4022105E-03 0.1673393 at 90iterations 1.9329637E-03 7.3542595E-02 at 100iterations 8.4996823E-04 3.3280373E-02 at 110iterations 3.7371568E-04 1.4001846E-02 at 120iterations finished qdiffx linear iterations at : 14:13:34 total time elapsed so far: 6.990000 # loops : 120 mean,max change (kT/e) : 3.7371568E-04 1.4001846E-02 energy calculations done at 6.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.160000 DelPhi exited at 14:13:37 7.163u 0.185s 0:28.71 25.5% 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 Nov 22 2011 at 14:13:39 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: 251 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1958 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: 2.698287 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): -8.939000 50.43200 ymin,ymax (A): 8.719001 51.55400 zmin,zma (A): -4.035000 38.82300 x,y,z range (A): 59.37100 42.83500 42.85800 scale (grids/A): 2.698287 object centre (A): 20.74650 30.13650 17.39400 number of atom coordinates read : 1958 total number of charged atoms : 1826 net assigned charge : 5.000012 assigned positive charge : 290.5560 centred at (gu) : 90.77859 85.96857 92.17920 assigned negative charge : -285.5562 centred at (gu) : 90.67445 85.54225 92.81712 start vw surface at 0.1100000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 119581 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17069 grid for indexing accessible points = 1.400000 m= 59334 mr = 85693 m= 19920 mr = 48918 m= 3652 mr = 16172 m= 274 mr = 2667 m= 3 mr = 126 m= 0 mr = 0 time to grow re-entrant surface = 0.5100000 no. cavity mid-points inaccessible to solvent = 1409 time to turn everything in is 0.9200000 number of dielectric boundary points 49188 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.050000 number of grid points assigned charge 14604 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) : 1.798858 object centre at (A) : 20.74650 30.13650 17.39400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.5262137E-02 1.4930434E-02 midg,1,midg; midg,igrid,midg 9.7682565E-02 6.1050292E-02 1,midg,midg; igrid,midg,midg 0.2915197 0.5469082 gauss-seidel spectral radius is 0.9991742 estimated iterations to convergence 275 setup time was (sec) 1.200000 now iterating at: 14:13:46 rms-change max change #iterations 7.731954 315.0647 at 10iterations 4.356827 110.1607 at 20iterations 2.438779 68.95322 at 30iterations 1.364152 30.02701 at 40iterations 0.7576051 20.14661 at 50iterations 0.4226492 9.095974 at 60iterations 0.2351745 6.003238 at 70iterations 0.1307053 2.794780 at 80iterations 7.2535686E-02 1.517805 at 90iterations 4.0350359E-02 0.8859959 at 100iterations 2.2447392E-02 0.4978340 at 110iterations 1.2499997E-02 0.2917485 at 120iterations 6.9355848E-03 0.1518240 at 130iterations 3.8447212E-03 8.6469173E-02 at 140iterations 2.1379052E-03 4.7629118E-02 at 150iterations 1.1866739E-03 2.6990891E-02 at 160iterations 6.5846543E-04 1.4143705E-02 at 170iterations 3.6581868E-04 9.2518330E-03 at 180iterations finished qdiffx linear iterations at : 14:14:15 total time elapsed so far: 10.95000 # loops : 180 mean,max change (kT/e) : 3.6581868E-04 9.2518330E-03 energy calculations done at 10.95000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.12000 DelPhi exited at 14:14:18 11.127u 0.184s 0:39.33 28.7% 0+0k 0+0io 0pf+0w