Mon Oct 10 19:32:29 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 19:32:29 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2945 !!! 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6218449 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): 14.36900 71.61800 ymin,ymax (A): 2.703000 51.78800 zmin,zma (A): 6.787000 62.70800 x,y,z range (A): 57.24900 49.08500 55.92100 scale (grids/A): 0.6218449 object centre (A): 42.99350 27.24550 34.74750 number of atom coordinates read : 2945 total number of charged atoms : 2804 net assigned charge : -2.485970 assigned positive charge : 445.3488 centred at (gu) : 89.21484 90.53068 91.16694 assigned negative charge : -447.8361 centred at (gu) : 89.18333 90.59068 91.21479 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7726 nv = 96 ne = 84 npr = 58855 no. pairs analyzed = 58855 no. exposed pairs = 3839 no. arc points = 27335 no. surface atoms = 1290 nbur = 1655 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 393 mr = 4095 m= 2 mr = 29 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 29 time to turn everything in is 0.2300000 number of dielectric boundary points 3997 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2725 ## 255 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 9367 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3923832E-09 -7.6289517E-09 midg,1,midg; midg,igrid,midg 2.4776434E-09 -7.7417273E-09 1,midg,midg; igrid,midg,midg -5.4193690E-09 4.2521914E-10 gauss-seidel spectral radius is 0.9866440 estimated iterations to convergence 71 setup time was (sec) 0.4200000 now iterating at: 19:32:29 rms-change max change #iterations 0.1367569 20.61122 at 10iterations 1.2775269E-02 1.811414 at 20iterations 1.2085487E-03 0.1645508 at 30iterations 1.2232644E-04 1.7780304E-02 at 40iterations 1.6588310E-05 2.9344559E-03 at 50iterations finished qdiffx linear iterations at : 19:32:32 total time elapsed so far: 3.300000 # loops : 50 mean,max change (kT/e) : 1.6588310E-05 2.9344559E-03 energy calculations done at 3.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.440000 DelPhi exited at 19:32:33 3.440u 0.163s 0:03.99 90.2% 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 19:32:33 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2945 !!! 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.865535 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): 14.36900 71.61800 ymin,ymax (A): 2.703000 51.78800 zmin,zma (A): 6.787000 62.70800 x,y,z range (A): 57.24900 49.08500 55.92100 scale (grids/A): 1.865535 object centre (A): 42.99350 27.24550 34.74750 number of atom coordinates read : 2945 total number of charged atoms : 2804 net assigned charge : -2.485970 assigned positive charge : 445.3488 centred at (gu) : 87.64370 91.59115 93.50011 assigned negative charge : -447.8361 centred at (gu) : 87.54964 91.77180 93.64417 start vw surface at 0.1000000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 82789 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27335 grid for indexing accessible points = 1.400000 m= 28938 mr = 56080 m= 4149 mr = 20756 m= 170 mr = 2421 m= 2 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4100000 number of dielectric boundary points 36760 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 162 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 22026 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) : 0.6218449 object centre at (A) : 42.99350 27.24550 34.74750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.7574511E-03 1.7030986E-02 midg,1,midg; midg,igrid,midg 5.2960119E-03 -2.7429419E-02 1,midg,midg; igrid,midg,midg -5.5031009E-02 1.3542133E-02 gauss-seidel spectral radius is 0.9986194 estimated iterations to convergence 213 setup time was (sec) 0.6300000 now iterating at: 19:32:34 rms-change max change #iterations 4.394381 169.3215 at 10iterations 2.039550 68.51009 at 20iterations 0.9493276 28.76882 at 30iterations 0.4408003 13.39193 at 40iterations 0.2055985 6.216702 at 50iterations 9.5954768E-02 3.496296 at 60iterations 4.4648536E-02 1.355602 at 70iterations 2.0744596E-02 0.6246510 at 80iterations 9.7037749E-03 0.3530197 at 90iterations 4.5265416E-03 0.1558132 at 100iterations 2.1114238E-03 7.5634003E-02 at 110iterations 9.8556792E-04 3.1844199E-02 at 120iterations finished qdiffx linear iterations at : 19:32:41 total time elapsed so far: 7.780000 # loops : 120 mean,max change (kT/e) : 9.8556792E-04 3.1844199E-02 energy calculations done at 7.780000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.920000 DelPhi exited at 19:32:42 7.920u 0.192s 0:09.37 86.5% 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 Mon Oct 10 2011 at 19:32:42 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2945 !!! 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.798302 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): 14.36900 71.61800 ymin,ymax (A): 2.703000 51.78800 zmin,zma (A): 6.787000 62.70800 x,y,z range (A): 57.24900 49.08500 55.92100 scale (grids/A): 2.798302 object centre (A): 42.99350 27.24550 34.74750 number of atom coordinates read : 2945 total number of charged atoms : 2804 net assigned charge : -2.485970 assigned positive charge : 445.3488 centred at (gu) : 86.46542 92.38642 95.24999 assigned negative charge : -447.8361 centred at (gu) : 86.32433 92.65762 95.46616 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 191434 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27335 grid for indexing accessible points = 1.400000 m= 94261 mr = 136266 m= 33140 mr = 75874 m= 7146 mr = 26036 m= 722 mr = 5142 m= 30 mr = 420 m= 0 mr = 2 time to grow re-entrant surface = 0.6000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.040000 number of dielectric boundary points 82993 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.140000 number of grid points assigned charge 22426 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) : 1.865535 object centre at (A) : 42.99350 27.24550 34.74750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1785578 0.3036597 midg,1,midg; midg,igrid,midg 6.2022395E-02 -0.3099227 1,midg,midg; igrid,midg,midg -0.6516298 0.2627340 gauss-seidel spectral radius is 0.9992771 estimated iterations to convergence 293 setup time was (sec) 1.280000 now iterating at: 19:32:44 rms-change max change #iterations 10.63642 321.1478 at 10iterations 6.320615 140.9952 at 20iterations 3.726100 92.07043 at 30iterations 2.186979 41.36024 at 40iterations 1.280594 26.37394 at 50iterations 0.7455610 16.34109 at 60iterations 0.4344667 8.087132 at 70iterations 0.2525407 4.714012 at 80iterations 0.1464146 2.946892 at 90iterations 8.4799483E-02 1.614447 at 100iterations 4.9208563E-02 0.9217052 at 110iterations 2.8482249E-02 0.5015907 at 120iterations 1.6525898E-02 0.3132439 at 130iterations 9.5440866E-03 0.1710625 at 140iterations 5.5266488E-03 0.1035728 at 150iterations 3.1936008E-03 5.9310913E-02 at 160iterations 1.8473589E-03 3.4551620E-02 at 170iterations 1.0673617E-03 2.0263672E-02 at 180iterations finished qdiffx linear iterations at : 19:32:55 total time elapsed so far: 12.78000 # loops : 180 mean,max change (kT/e) : 1.0673617E-03 2.0263672E-02 energy calculations done at 12.78000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.91000 DelPhi exited at 19:32:56 12.914u 0.213s 0:13.52 97.0% 0+0k 0+0io 0pf+0w