Tue Oct 11 02:23:04 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+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 Tue Oct 11 2011 at 02:23:04 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2636 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6661801 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): 24.01700 70.22400 ymin,ymax (A): 14.43200 67.87100 zmin,zma (A): 10.34200 58.23000 x,y,z range (A): 46.20700 53.43900 47.88800 scale (grids/A): 0.6661801 object centre (A): 47.12050 41.15150 34.28600 number of atom coordinates read : 2636 total number of charged atoms : 2501 net assigned charge : 3.500005 assigned positive charge : 403.5325 centred at (gu) : 88.83852 90.36089 89.94814 assigned negative charge : -400.0334 centred at (gu) : 88.99328 90.62312 89.88999 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7862 nv = 96 ne = 84 npr = 53879 no. pairs analyzed = 53879 no. exposed pairs = 3307 no. arc points = 22348 no. surface atoms = 1114 nbur = 1522 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 446 mr = 4434 m= 3 mr = 64 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3813 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2087 ## 167 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 9164 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.5964609E-09 2.3913783E-08 midg,1,midg; midg,igrid,midg 6.6049353E-08 -5.8190810E-08 1,midg,midg; igrid,midg,midg 5.9540074E-08 -2.1136147E-08 gauss-seidel spectral radius is 0.9883232 estimated iterations to convergence 76 setup time was (sec) 0.5900000 now iterating at: 02:23:05 rms-change max change #iterations 0.1748651 28.05996 at 10iterations 2.1410065E-02 2.689873 at 20iterations 4.6385322E-03 0.6929321 at 30iterations 1.7824635E-03 0.2770538 at 40iterations 7.5196871E-04 0.1166763 at 50iterations finished qdiffx linear iterations at : 02:23:08 total time elapsed so far: 4.020000 # loops : 50 mean,max change (kT/e) : 7.5196871E-04 0.1166763 energy calculations done at 4.020000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.200000 DelPhi exited at 02:23:09 4.201u 0.349s 0:05.45 83.3% 0+0k 0+0io 3pf+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 02:23:09 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2636 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.998540 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): 24.01700 70.22400 ymin,ymax (A): 14.43200 67.87100 zmin,zma (A): 10.34200 58.23000 x,y,z range (A): 46.20700 53.43900 47.88800 scale (grids/A): 1.998540 object centre (A): 47.12050 41.15150 34.28600 number of atom coordinates read : 2636 total number of charged atoms : 2501 net assigned charge : 3.500005 assigned positive charge : 403.5325 centred at (gu) : 86.51486 91.08208 89.84389 assigned negative charge : -400.0334 centred at (gu) : 86.97954 91.86913 89.66987 start vw surface at 0.1600000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 84649 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22348 grid for indexing accessible points = 1.400000 m= 31587 mr = 59627 m= 5429 mr = 23550 m= 380 mr = 3470 m= 7 mr = 147 m= 0 mr = 0 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7600000 number of dielectric boundary points 35258 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 81 iepsmp to db, and charging done at 0.9000000 number of grid points assigned charge 19765 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) : 0.6661801 object centre at (A) : 47.12050 41.15150 34.28600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.9718615E-02 -9.5997276E-03 midg,1,midg; midg,igrid,midg 7.0065171E-02 -6.5555118E-02 1,midg,midg; igrid,midg,midg 5.1421810E-02 -1.5976818E-02 gauss-seidel spectral radius is 0.9987605 estimated iterations to convergence 225 setup time was (sec) 1.060000 now iterating at: 02:23:11 rms-change max change #iterations 4.767249 209.3106 at 10iterations 2.323681 77.78771 at 20iterations 1.129509 34.55011 at 30iterations 0.5494875 16.55246 at 40iterations 0.2693060 7.806374 at 50iterations 0.1315883 4.077101 at 60iterations 6.4493403E-02 1.939293 at 70iterations 3.2246858E-02 0.9504495 at 80iterations 1.6549019E-02 0.5186157 at 90iterations 9.0337908E-03 0.3190575 at 100iterations 5.3599402E-03 0.1967468 at 110iterations 3.4911025E-03 0.1200638 at 120iterations finished qdiffx linear iterations at : 02:23:20 total time elapsed so far: 9.880000 # loops : 120 mean,max change (kT/e) : 3.4911025E-03 0.1200638 energy calculations done at 9.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.08000 DelPhi exited at 02:23:20 10.079u 0.336s 0:10.88 95.5% 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 Oct 11 2011 at 02:23:20 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2636 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.997810 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): 24.01700 70.22400 ymin,ymax (A): 14.43200 67.87100 zmin,zma (A): 10.34200 58.23000 x,y,z range (A): 46.20700 53.43900 47.88800 scale (grids/A): 2.997810 object centre (A): 47.12050 41.15150 34.28600 number of atom coordinates read : 2636 total number of charged atoms : 2501 net assigned charge : 3.500005 assigned positive charge : 403.5325 centred at (gu) : 84.77213 91.62290 89.76559 assigned negative charge : -400.0334 centred at (gu) : 85.46916 92.80361 89.50470 start vw surface at 0.1700000 fill in re-entrant regions at 0.6600000 boundary points on vw surface= 195408 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22348 grid for indexing accessible points = 1.400000 m= 100661 mr = 144091 m= 38068 mr = 82731 m= 9943 mr = 30859 m= 1638 mr = 7516 m= 108 mr = 1086 m= 5 mr = 47 m= 0 mr = 0 time to grow re-entrant surface = 1.220000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.000000 number of dielectric boundary points 79501 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.160000 number of grid points assigned charge 20008 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) : 1.998540 object centre at (A) : 47.12050 41.15150 34.28600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3303789 -0.1646202 midg,1,midg; midg,igrid,midg 0.9661055 -0.8479881 1,midg,midg; igrid,midg,midg 0.3909207 -0.1508040 gauss-seidel spectral radius is 0.9992912 estimated iterations to convergence 296 setup time was (sec) 2.340000 now iterating at: 02:23:23 rms-change max change #iterations 10.90652 407.3394 at 10iterations 6.437527 152.6983 at 20iterations 3.797808 74.21831 at 30iterations 2.231831 46.64413 at 40iterations 1.311093 23.84601 at 50iterations 0.7679005 16.72300 at 60iterations 0.4498433 9.422302 at 70iterations 0.2631516 4.688913 at 80iterations 0.1536565 2.393906 at 90iterations 9.0105362E-02 1.666369 at 100iterations 5.2756712E-02 0.9688568 at 110iterations 3.1070774E-02 0.5555611 at 120iterations 1.8471511E-02 0.3237419 at 130iterations 1.1220483E-02 0.2377701 at 140iterations 7.1161245E-03 0.1429749 at 150iterations 4.7768694E-03 9.6397400E-02 at 160iterations 3.4598133E-03 7.5065613E-02 at 170iterations 2.6795161E-03 5.3892136E-02 at 180iterations finished qdiffx linear iterations at : 02:23:38 total time elapsed so far: 17.13000 # loops : 180 mean,max change (kT/e) : 2.6795161E-03 5.3892136E-02 energy calculations done at 17.13000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.33000 DelPhi exited at 02:23:38 17.327u 0.338s 0:17.94 98.3% 0+0k 0+0io 0pf+0w