Sun Oct 9 07:20:26 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 Sun Oct 9 2011 at 07:20:26 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1697 !!! WARNING: NAP 164 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6994244 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): -9.016000 33.83300 ymin,ymax (A): 2.370000 43.14500 zmin,zma (A): 9.492001 60.39100 x,y,z range (A): 42.84900 40.77500 50.89900 scale (grids/A): 0.6994244 object centre (A): 12.40850 22.75750 34.94150 number of atom coordinates read : 1697 total number of charged atoms : 1560 net assigned charge : -11.49999 assigned positive charge : 251.0242 centred at (gu) : 91.92416 89.45284 89.48224 assigned negative charge : -262.5241 centred at (gu) : 91.69566 89.63603 89.70650 start vw surface at 0.1300000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 5531 nv = 96 ne = 84 npr = 36981 no. pairs analyzed = 36981 no. exposed pairs = 2107 no. arc points = 14687 no. surface atoms = 721 nbur = 976 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 335 mr = 3065 m= 2 mr = 59 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 2744 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1253 ## 89 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 6150 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.2866401E-09 -1.4595264E-07 midg,1,midg; midg,igrid,midg -2.1535392E-08 -1.3184962E-07 1,midg,midg; igrid,midg,midg -1.1228136E-07 -4.3579731E-09 gauss-seidel spectral radius is 0.9893109 estimated iterations to convergence 79 setup time was (sec) 0.5200000 now iterating at: 07:20:27 rms-change max change #iterations 0.1749532 43.30707 at 10iterations 2.0884380E-02 3.189245 at 20iterations 2.5235659E-03 0.3818645 at 30iterations 2.9719219E-04 5.4541826E-02 at 40iterations 3.5812456E-05 5.3062439E-03 at 50iterations finished qdiffx linear iterations at : 07:20:30 total time elapsed so far: 3.720000 # loops : 50 mean,max change (kT/e) : 3.5812456E-05 5.3062439E-03 energy calculations done at 3.720000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.900000 DelPhi exited at 07:20:31 3.904u 0.261s 0:04.44 93.6% 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 Sun Oct 9 2011 at 07:20:31 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1697 !!! WARNING: NAP 164 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.098273 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): -9.016000 33.83300 ymin,ymax (A): 2.370000 43.14500 zmin,zma (A): 9.492001 60.39100 x,y,z range (A): 42.84900 40.77500 50.89900 scale (grids/A): 2.098273 object centre (A): 12.40850 22.75750 34.94150 number of atom coordinates read : 1697 total number of charged atoms : 1560 net assigned charge : -11.49999 assigned positive charge : 251.0242 centred at (gu) : 95.77269 88.35863 88.44668 assigned negative charge : -262.5241 centred at (gu) : 95.08712 88.90807 89.11954 start vw surface at 0.1200000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 58001 reading accessible surface arcs data from file ARCDAT no. of arc points read = 14687 grid for indexing accessible points = 1.400000 m= 22969 mr = 39815 m= 4334 mr = 17541 m= 276 mr = 2818 m= 9 mr = 107 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4600000 number of dielectric boundary points 25308 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 43 iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 12417 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) : 0.6994244 object centre at (A) : 12.40850 22.75750 34.94150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.1579932E-02 -8.5335843E-02 midg,1,midg; midg,igrid,midg -9.8808398E-03 -4.6951450E-02 1,midg,midg; igrid,midg,midg -6.9274969E-02 -5.7662744E-03 gauss-seidel spectral radius is 0.9987677 estimated iterations to convergence 226 setup time was (sec) 0.7900000 now iterating at: 07:20:32 rms-change max change #iterations 4.154867 278.2935 at 10iterations 2.009048 77.64287 at 20iterations 0.9776472 34.46649 at 30iterations 0.4770914 19.59168 at 40iterations 0.2324047 8.499025 at 50iterations 0.1129973 3.882540 at 60iterations 5.5023316E-02 1.910110 at 70iterations 2.6671514E-02 0.8872776 at 80iterations 1.2953388E-02 0.4457550 at 90iterations 6.3010138E-03 0.2086487 at 100iterations 3.0894431E-03 9.7354889E-02 at 110iterations 1.4969232E-03 4.9526215E-02 at 120iterations finished qdiffx linear iterations at : 07:20:39 total time elapsed so far: 8.070000 # loops : 120 mean,max change (kT/e) : 1.4969232E-03 4.9526215E-02 energy calculations done at 8.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.250000 DelPhi exited at 07:20:39 8.248u 0.346s 0:08.90 96.4% 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 Sun Oct 9 2011 at 07:20:40 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1697 !!! WARNING: NAP 164 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.147410 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): -9.016000 33.83300 ymin,ymax (A): 2.370000 43.14500 zmin,zma (A): 9.492001 60.39100 x,y,z range (A): 42.84900 40.77500 50.89900 scale (grids/A): 3.147410 object centre (A): 12.40850 22.75750 34.94150 number of atom coordinates read : 1697 total number of charged atoms : 1560 net assigned charge : -11.49999 assigned positive charge : 251.0242 centred at (gu) : 98.65907 87.53790 87.67003 assigned negative charge : -262.5241 centred at (gu) : 97.63068 88.36212 88.67935 start vw surface at 0.1300000 fill in re-entrant regions at 0.6600000 boundary points on vw surface= 133631 reading accessible surface arcs data from file ARCDAT no. of arc points read = 14687 grid for indexing accessible points = 1.400000 m= 71099 mr = 96080 m= 30004 mr = 59008 m= 8002 mr = 25007 m= 1167 mr = 6084 m= 106 mr = 730 m= 5 mr = 63 m= 0 mr = 0 time to grow re-entrant surface = 0.6500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.420000 number of dielectric boundary points 57042 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.550000 number of grid points assigned charge 12480 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) : 2.098273 object centre at (A) : 12.40850 22.75750 34.94150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1296185 -0.7013111 midg,1,midg; midg,igrid,midg -0.1196524 -0.3574907 1,midg,midg; igrid,midg,midg -0.6343885 -5.0827216E-02 gauss-seidel spectral radius is 0.9992753 estimated iterations to convergence 293 setup time was (sec) 1.780000 now iterating at: 07:20:42 rms-change max change #iterations 9.293202 371.3348 at 10iterations 5.358792 189.9951 at 20iterations 3.108289 72.67987 at 30iterations 1.799709 41.89178 at 40iterations 1.044792 23.51012 at 50iterations 0.6044440 12.79681 at 60iterations 0.3500970 7.431281 at 70iterations 0.2020354 3.821434 at 80iterations 0.1171577 2.300337 at 90iterations 6.7619108E-02 1.271652 at 100iterations 3.9095800E-02 0.7500094 at 110iterations 2.2585422E-02 0.4436743 at 120iterations 1.3030543E-02 0.2388918 at 130iterations 7.5237062E-03 0.1417847 at 140iterations 4.3495959E-03 8.8581085E-02 at 150iterations 2.5105132E-03 4.7007084E-02 at 160iterations 1.4495455E-03 2.8778076E-02 at 170iterations 8.3679159E-04 1.5918732E-02 at 180iterations finished qdiffx linear iterations at : 07:20:53 total time elapsed so far: 13.51000 # loops : 180 mean,max change (kT/e) : 8.3679159E-04 1.5918732E-02 energy calculations done at 13.51000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.68000 DelPhi exited at 07:20:54 13.683u 0.349s 0:14.32 97.9% 0+0k 0+0io 0pf+0w