Tue Oct 11 07:50:46 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 07:50:46 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2765 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.6363734 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): -13.57300 42.36900 ymin,ymax (A): -21.77400 28.18600 zmin,zma (A): -11.63500 40.18500 x,y,z range (A): 55.94200 49.96000 51.82000 scale (grids/A): 0.6363734 object centre (A): 14.39800 3.205999 14.27500 number of atom coordinates read : 2765 total number of charged atoms : 2402 net assigned charge : 10.50002 assigned positive charge : 386.1190 centred at (gu) : 90.13263 87.76543 90.92070 assigned negative charge : -375.6197 centred at (gu) : 90.10681 87.71288 91.14172 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 6759 nv = 96 ne = 84 npr = 51493 no. pairs analyzed = 51493 no. exposed pairs = 2941 no. arc points = 20634 no. surface atoms = 1005 nbur = 1760 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 320 mr = 3825 m= 1 mr = 33 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 15 time to turn everything in is 0.3500000 number of dielectric boundary points 3222 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2123 ## 239 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 8153 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.9546637E-08 -1.1108042E-08 midg,1,midg; midg,igrid,midg 1.3712033E-08 1.2165924E-08 1,midg,midg; igrid,midg,midg 1.1136637E-08 1.7154166E-08 gauss-seidel spectral radius is 0.9871961 estimated iterations to convergence 72 setup time was (sec) 0.5900000 now iterating at: 07:50:47 rms-change max change #iterations 0.1413782 23.06427 at 10iterations 1.3945548E-02 2.407959 at 20iterations 1.5865479E-03 0.2199097 at 30iterations 2.3203797E-04 3.2192230E-02 at 40iterations 4.5472501E-05 6.7329407E-03 at 50iterations finished qdiffx linear iterations at : 07:50:50 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 4.5472501E-05 6.7329407E-03 energy calculations done at 3.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.400000 DelPhi exited at 07:50:50 3.407u 0.123s 0:04.17 84.4% 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 07:50:50 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2765 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 1.909120 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): -13.57300 42.36900 ymin,ymax (A): -21.77400 28.18600 zmin,zma (A): -11.63500 40.18500 x,y,z range (A): 55.94200 49.96000 51.82000 scale (grids/A): 1.909120 object centre (A): 14.39800 3.205999 14.27500 number of atom coordinates read : 2765 total number of charged atoms : 2402 net assigned charge : 10.50002 assigned positive charge : 386.1190 centred at (gu) : 90.39735 83.29584 92.76174 assigned negative charge : -375.6197 centred at (gu) : 90.32005 83.13844 93.42479 start vw surface at 0.2400000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 72823 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20634 grid for indexing accessible points = 1.400000 m= 27107 mr = 51440 m= 4034 mr = 20504 m= 213 mr = 2541 m= 4 mr = 84 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 528 time to turn everything in is 0.6300000 number of dielectric boundary points 29612 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 163 iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 18860 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) : 0.6363734 object centre at (A) : 14.39800 3.205999 14.27500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.5716552E-02 -1.0007952E-02 midg,1,midg; midg,igrid,midg 1.3397514E-02 2.5370441E-02 1,midg,midg; igrid,midg,midg 2.2599012E-02 4.4556357E-02 gauss-seidel spectral radius is 0.9986250 estimated iterations to convergence 214 setup time was (sec) 0.9300000 now iterating at: 07:50:51 rms-change max change #iterations 4.138668 211.2398 at 10iterations 1.937721 67.36819 at 20iterations 0.9081929 28.85394 at 30iterations 0.4245889 13.39610 at 40iterations 0.1993879 6.504003 at 50iterations 9.3245313E-02 2.960079 at 60iterations 4.3676570E-02 1.458864 at 70iterations 2.0526089E-02 0.7249222 at 80iterations 9.6269855E-03 0.3085284 at 90iterations 4.5424984E-03 0.1441154 at 100iterations 2.1516557E-03 7.4266434E-02 at 110iterations 1.0305862E-03 3.4214020E-02 at 120iterations finished qdiffx linear iterations at : 07:50:58 total time elapsed so far: 7.560000 # loops : 120 mean,max change (kT/e) : 1.0305862E-03 3.4214020E-02 energy calculations done at 7.560000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.740000 DelPhi exited at 07:50:59 7.741u 0.193s 0:08.54 92.8% 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 Tue Oct 11 2011 at 07:50:59 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2765 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.863680 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): -13.57300 42.36900 ymin,ymax (A): -21.77400 28.18600 zmin,zma (A): -11.63500 40.18500 x,y,z range (A): 55.94200 49.96000 51.82000 scale (grids/A): 2.863680 object centre (A): 14.39800 3.205999 14.27500 number of atom coordinates read : 2765 total number of charged atoms : 2402 net assigned charge : 10.50002 assigned positive charge : 386.1190 centred at (gu) : 90.59573 79.94355 94.14249 assigned negative charge : -375.6197 centred at (gu) : 90.47997 79.70758 95.13708 start vw surface at 0.2200000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 168447 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20634 grid for indexing accessible points = 1.400000 m= 87684 mr = 124161 m= 31793 mr = 73123 m= 7332 mr = 25891 m= 997 mr = 5500 m= 53 mr = 729 m= 1 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.8100001 no. cavity mid-points inaccessible to solvent = 1941 time to turn everything in is 1.450000 number of dielectric boundary points 66885 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.580000 number of grid points assigned charge 19213 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) : 1.909120 object centre at (A) : 14.39800 3.205999 14.27500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.7211407 -0.1845545 midg,1,midg; midg,igrid,midg 0.1159024 0.2606103 1,midg,midg; igrid,midg,midg 0.1606931 0.3193767 gauss-seidel spectral radius is 0.9992453 estimated iterations to convergence 287 setup time was (sec) 1.740000 now iterating at: 07:51:01 rms-change max change #iterations 9.629771 328.5923 at 10iterations 5.574631 148.4320 at 20iterations 3.213931 64.53122 at 30iterations 1.849238 34.84578 at 40iterations 1.059909 19.40289 at 50iterations 0.6088327 11.61406 at 60iterations 0.3482683 6.579473 at 70iterations 0.1999124 3.630844 at 80iterations 0.1145969 2.209283 at 90iterations 6.5527350E-02 1.181319 at 100iterations 3.7517298E-02 0.6896434 at 110iterations 2.1581396E-02 0.3975105 at 120iterations 1.2434656E-02 0.2282867 at 130iterations 7.2222073E-03 0.1295586 at 140iterations 4.2279917E-03 7.9975128E-02 at 150iterations 2.5261291E-03 5.1731110E-02 at 160iterations 1.5471852E-03 2.8430939E-02 at 170iterations 9.8547537E-04 1.9496918E-02 at 180iterations finished qdiffx linear iterations at : 07:51:11 total time elapsed so far: 11.73000 # loops : 180 mean,max change (kT/e) : 9.8547537E-04 1.9496918E-02 energy calculations done at 11.73000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.91000 DelPhi exited at 07:51:11 11.915u 0.200s 0:12.43 97.4% 0+0k 0+0io 0pf+0w