Tue Oct 11 08:32:42 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 08:32:42 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: 325 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2051 !!! WARNING: HIR 40 has a net charge of 0.5140 !!! WARNING: SEP 172 has a net charge of -0.4750 !!! WARNING: SEP 177 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: 0.7152328 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): -4.279000 45.49500 ymin,ymax (A): 38.48700 85.61500 zmin,zma (A): -13.50100 28.76200 x,y,z range (A): 49.77400 47.12800 42.26300 scale (grids/A): 0.7152328 object centre (A): 20.60800 62.05100 7.630499 number of atom coordinates read : 2051 total number of charged atoms : 1988 net assigned charge : 5.564012 assigned positive charge : 325.7420 centred at (gu) : 90.71558 91.00140 90.31358 assigned negative charge : -320.1781 centred at (gu) : 90.64799 90.89975 90.39044 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.0000000E-02 boundary points on vw surface= 7296 nv = 96 ne = 84 npr = 39759 no. pairs analyzed = 39759 no. exposed pairs = 2522 no. arc points = 17315 no. surface atoms = 872 nbur = 1179 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 505 mr = 4231 m= 2 mr = 86 m= 0 mr = 0 time to grow re-entrant surface = 8.0000013E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1700000 number of dielectric boundary points 3486 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1673 ## 149 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 8118 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.5509989E-08 9.1796073E-09 midg,1,midg; midg,igrid,midg -4.6638191E-09 1.4084436E-07 1,midg,midg; igrid,midg,midg 1.3011134E-08 1.0999873E-07 gauss-seidel spectral radius is 0.9898077 estimated iterations to convergence 81 setup time was (sec) 0.3500000 now iterating at: 08:32:42 rms-change max change #iterations 0.2165906 30.48700 at 10iterations 2.8031001E-02 3.618149 at 20iterations 3.8650439E-03 0.5824013 at 30iterations 6.5903948E-04 8.5760117E-02 at 40iterations 1.6112234E-04 2.1017075E-02 at 50iterations finished qdiffx linear iterations at : 08:32:45 total time elapsed so far: 3.190000 # loops : 50 mean,max change (kT/e) : 1.6112234E-04 2.1017075E-02 energy calculations done at 3.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.320000 DelPhi exited at 08:32:46 3.328u 0.187s 0:03.82 91.6% 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 Tue Oct 11 2011 at 08:32:46 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: 325 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2051 !!! WARNING: HIR 40 has a net charge of 0.5140 !!! WARNING: SEP 172 has a net charge of -0.4750 !!! WARNING: SEP 177 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: 2.145699 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): -4.279000 45.49500 ymin,ymax (A): 38.48700 85.61500 zmin,zma (A): -13.50100 28.76200 x,y,z range (A): 49.77400 47.12800 42.26300 scale (grids/A): 2.145699 object centre (A): 20.60800 62.05100 7.630499 number of atom coordinates read : 2051 total number of charged atoms : 1988 net assigned charge : 5.564012 assigned positive charge : 325.7420 centred at (gu) : 92.14690 93.00416 90.94077 assigned negative charge : -320.1781 centred at (gu) : 91.94409 92.69916 91.17146 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 77139 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17315 grid for indexing accessible points = 1.400000 m= 31188 mr = 54903 m= 5966 mr = 23695 m= 531 mr = 3929 m= 19 mr = 279 m= 0 mr = 3 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4000000 number of dielectric boundary points 32034 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 63 iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 15789 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) : 0.7152328 object centre at (A) : 20.60800 62.05100 7.630499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.4506813E-02 1.8602800E-02 midg,1,midg; midg,igrid,midg -3.7014045E-02 2.8761972E-02 1,midg,midg; igrid,midg,midg 4.2144105E-02 5.2763052E-02 gauss-seidel spectral radius is 0.9988528 estimated iterations to convergence 234 setup time was (sec) 0.6200000 now iterating at: 08:32:46 rms-change max change #iterations 4.772034 236.1834 at 10iterations 2.369751 84.50015 at 20iterations 1.186802 36.27531 at 30iterations 0.5925696 19.67965 at 40iterations 0.2964796 8.496998 at 50iterations 0.1476806 4.269360 at 60iterations 7.4091859E-02 2.230032 at 70iterations 3.7286777E-02 1.117512 at 80iterations 1.8773681E-02 0.5582619 at 90iterations 9.5117735E-03 0.2684288 at 100iterations 4.8553552E-03 0.1571159 at 110iterations 2.5504485E-03 7.4454308E-02 at 120iterations finished qdiffx linear iterations at : 08:32:53 total time elapsed so far: 7.660000 # loops : 120 mean,max change (kT/e) : 2.5504485E-03 7.4454308E-02 energy calculations done at 7.660000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.800000 DelPhi exited at 08:32:54 7.800u 0.182s 0:08.42 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 08:32:54 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: 325 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2051 !!! WARNING: HIR 40 has a net charge of 0.5140 !!! WARNING: SEP 172 has a net charge of -0.4750 !!! WARNING: SEP 177 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: 3.218548 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): -4.279000 45.49500 ymin,ymax (A): 38.48700 85.61500 zmin,zma (A): -13.50100 28.76200 x,y,z range (A): 49.77400 47.12800 42.26300 scale (grids/A): 3.218548 object centre (A): 20.60800 62.05100 7.630499 number of atom coordinates read : 2051 total number of charged atoms : 1988 net assigned charge : 5.564012 assigned positive charge : 325.7420 centred at (gu) : 93.22041 94.50616 91.41108 assigned negative charge : -320.1781 centred at (gu) : 92.91618 94.04874 91.75713 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 177855 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17315 grid for indexing accessible points = 1.400000 m= 97342 mr = 132168 m= 39427 mr = 81249 m= 11195 mr = 32306 m= 2294 mr = 8637 m= 294 mr = 1662 m= 14 mr = 194 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 1.180000 number of dielectric boundary points 72205 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.270000 number of grid points assigned charge 15904 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) : 2.145699 object centre at (A) : 20.60800 62.05100 7.630499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1584235 0.1617936 midg,1,midg; midg,igrid,midg -0.4327407 0.2464500 1,midg,midg; igrid,midg,midg 0.2033261 0.4458928 gauss-seidel spectral radius is 0.9993063 estimated iterations to convergence 300 setup time was (sec) 1.410000 now iterating at: 08:32:56 rms-change max change #iterations 10.57256 398.6182 at 10iterations 6.247781 134.1430 at 20iterations 3.693985 64.30096 at 30iterations 2.182326 42.93742 at 40iterations 1.284166 24.88670 at 50iterations 0.7557867 13.68792 at 60iterations 0.4452274 7.860031 at 70iterations 0.2618230 4.846994 at 80iterations 0.1539443 2.722477 at 90iterations 9.0553418E-02 1.615940 at 100iterations 5.3526841E-02 0.9649105 at 110iterations 3.1730969E-02 0.5989456 at 120iterations 1.9002851E-02 0.3819427 at 130iterations 1.1602311E-02 0.2089310 at 140iterations 7.2927773E-03 0.1325188 at 150iterations 4.7830502E-03 9.5321655E-02 at 160iterations 3.3250363E-03 6.3419342E-02 at 170iterations 2.4393594E-03 4.6943665E-02 at 180iterations finished qdiffx linear iterations at : 08:33:07 total time elapsed so far: 12.61000 # loops : 180 mean,max change (kT/e) : 2.4393594E-03 4.6943665E-02 energy calculations done at 12.61000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.75000 DelPhi exited at 08:33:07 12.750u 0.205s 0:13.41 96.5% 0+0k 0+0io 0pf+0w