Mon Oct 10 17:03:56 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 17:03:56 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: 310 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2754 !!! WARNING: HIT 107 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5591945 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): -13.87500 49.78800 ymin,ymax (A): -26.48400 18.14300 zmin,zma (A): -42.08800 5.454000 x,y,z range (A): 63.66300 44.62700 47.54200 scale (grids/A): 0.5591945 object centre (A): 17.95650 -4.170500 -18.31700 number of atom coordinates read : 2754 total number of charged atoms : 2614 net assigned charge : -0.4859678 assigned positive charge : 416.2843 centred at (gu) : 89.65974 89.67255 89.29372 assigned negative charge : -416.7713 centred at (gu) : 89.72778 89.54485 89.18715 start vw surface at 0.1600000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 5691 nv = 96 ne = 84 npr = 54680 no. pairs analyzed = 54680 no. exposed pairs = 3711 no. arc points = 26383 no. surface atoms = 1247 nbur = 1507 mkacc time = 0.1300000 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 = 1.540000 m= 224 mr = 2797 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 3111 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2676 ## 342 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 7354 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.3425226E-09 8.6049406E-10 midg,1,midg; midg,igrid,midg -1.4602253E-09 1.1354145E-09 1,midg,midg; igrid,midg,midg 6.9969847E-10 -6.7172012E-10 gauss-seidel spectral radius is 0.9834937 estimated iterations to convergence 64 setup time was (sec) 0.5600000 now iterating at: 17:03:57 rms-change max change #iterations 8.0016948E-02 13.99636 at 10iterations 5.6476514E-03 0.8308449 at 20iterations 3.9977336E-04 7.3354721E-02 at 30iterations 2.8707680E-05 4.9066544E-03 at 40iterations 2.0651971E-06 3.5238266E-04 at 50iterations finished qdiffx linear iterations at : 17:03:59 total time elapsed so far: 3.310000 # loops : 50 mean,max change (kT/e) : 2.0651971E-06 3.5238266E-04 energy calculations done at 3.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.510000 DelPhi exited at 17:04:00 3.510u 0.177s 0:04.61 79.8% 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 17:04:01 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: 310 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2754 !!! WARNING: HIT 107 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.677583 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): -13.87500 49.78800 ymin,ymax (A): -26.48400 18.14300 zmin,zma (A): -42.08800 5.454000 x,y,z range (A): 63.66300 44.62700 47.54200 scale (grids/A): 1.677583 object centre (A): 17.95650 -4.170500 -18.31700 number of atom coordinates read : 2754 total number of charged atoms : 2614 net assigned charge : -0.4859678 assigned positive charge : 416.2843 centred at (gu) : 88.97838 89.01694 87.88042 assigned negative charge : -416.7713 centred at (gu) : 89.18308 88.63411 87.56108 start vw surface at 0.1600000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 62401 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26383 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 18926 mr = 40830 m= 2004 mr = 12796 m= 71 mr = 886 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 513 time to turn everything in is 0.4900000 number of dielectric boundary points 28890 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 272 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 20132 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) : 0.5591945 object centre at (A) : 17.95650 -4.170500 -18.31700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.2439203E-02 6.8311621E-03 midg,1,midg; midg,igrid,midg -4.9180486E-03 2.8825386E-03 1,midg,midg; igrid,midg,midg 1.3754335E-03 -4.6698363E-03 gauss-seidel spectral radius is 0.9982678 estimated iterations to convergence 191 setup time was (sec) 0.7900000 now iterating at: 17:04:02 rms-change max change #iterations 3.414348 171.9026 at 10iterations 1.443512 65.19354 at 20iterations 0.6155689 23.12100 at 30iterations 0.2608236 10.61640 at 40iterations 0.1111789 4.120712 at 50iterations 4.7307651E-02 1.688408 at 60iterations 2.0129757E-02 0.7650452 at 70iterations 8.5571334E-03 0.3418350 at 80iterations 3.6401437E-03 0.1314316 at 90iterations 1.5501109E-03 6.1069489E-02 at 100iterations 6.5802177E-04 2.5382996E-02 at 110iterations 2.8129845E-04 9.4985962E-03 at 120iterations finished qdiffx linear iterations at : 17:04:08 total time elapsed so far: 7.490000 # loops : 120 mean,max change (kT/e) : 2.8129845E-04 9.4985962E-03 energy calculations done at 7.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.670000 DelPhi exited at 17:04:11 7.674u 0.241s 0:10.11 78.2% 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 17:04:11 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: 310 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2754 !!! WARNING: HIT 107 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.516375 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): -13.87500 49.78800 ymin,ymax (A): -26.48400 18.14300 zmin,zma (A): -42.08800 5.454000 x,y,z range (A): 63.66300 44.62700 47.54200 scale (grids/A): 2.516375 object centre (A): 17.95650 -4.170500 -18.31700 number of atom coordinates read : 2754 total number of charged atoms : 2614 net assigned charge : -0.4859678 assigned positive charge : 416.2843 centred at (gu) : 88.46738 88.52522 86.82037 assigned negative charge : -416.7713 centred at (gu) : 88.77460 87.95123 86.34161 start vw surface at 0.1600000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 144707 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26383 grid for indexing accessible points = 1.400000 m= 64907 mr = 100203 m= 18872 mr = 50413 m= 3044 mr = 13951 m= 229 mr = 1855 m= 2 mr = 89 m= 0 mr = 0 time to grow re-entrant surface = 0.6400000 no. cavity mid-points inaccessible to solvent = 1801 time to turn everything in is 1.130000 number of dielectric boundary points 65250 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 15 iepsmp to db, and charging done at 1.260000 number of grid points assigned charge 20895 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) : 1.677583 object centre at (A) : 17.95650 -4.170500 -18.31700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1721684 0.1059026 midg,1,midg; midg,igrid,midg -6.2945895E-02 1.9100053E-02 1,midg,midg; igrid,midg,midg 4.9267158E-02 0.3607655 gauss-seidel spectral radius is 0.9991674 estimated iterations to convergence 274 setup time was (sec) 1.440000 now iterating at: 17:04:12 rms-change max change #iterations 8.891912 387.5951 at 10iterations 5.059349 131.4108 at 20iterations 2.854625 81.84259 at 30iterations 1.608150 41.76386 at 40iterations 0.9037578 21.43088 at 50iterations 0.5052105 12.11482 at 60iterations 0.2819096 7.106730 at 70iterations 0.1570761 3.416176 at 80iterations 8.7369405E-02 1.876136 at 90iterations 4.8847951E-02 0.9744205 at 100iterations 2.7107067E-02 0.6493645 at 110iterations 1.5029914E-02 0.3106623 at 120iterations 8.3348034E-03 0.1562073 at 130iterations 4.6402547E-03 9.2279434E-02 at 140iterations 2.5712983E-03 5.5950165E-02 at 150iterations 1.4290034E-03 2.9396057E-02 at 160iterations 7.9117971E-04 1.5884399E-02 at 170iterations 4.3983455E-04 8.5682869E-03 at 180iterations finished qdiffx linear iterations at : 17:04:23 total time elapsed so far: 12.45000 # loops : 180 mean,max change (kT/e) : 4.3983455E-04 8.5682869E-03 energy calculations done at 12.45000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.65000 DelPhi exited at 17:04:25 12.654u 0.228s 0:14.03 91.7% 0+0k 0+0io 0pf+0w