Thu Jan 19 11:42:40 PST 2012 #!/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 Thu Jan 19 2012 at 11:42:40 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5095 !!! WARNING: LYS 37 has a net charge of 0.0200 !!! WARNING: TYR 44 has a net charge of 0.0210 !!! WARNING: ARG 54 has a net charge of 0.0400 !!! WARNING: CYS 125 has a net charge of -0.1350 !!! WARNING: CYS 128 has a net charge of -0.1350 !!! WARNING: CYS 157 has a net charge of -0.1350 !!! WARNING: CYS 160 has a net charge of -0.1350 !!! WARNING: LYS 200 has a net charge of 0.0200 !!! WARNING: ARG 214 has a net charge of 0.0400 !!! WARNING: CYS 285 has a net charge of -0.1350 !!! WARNING: CYS 288 has a net charge of -0.1350 !!! WARNING: CYS 317 has a net charge of -0.1350 !!! WARNING: CYS 320 has a net charge of -0.1350 !!! WARNING: CYS 448 has a net charge of -0.1350 !!! WARNING: CYS 451 has a net charge of -0.1350 !!! WARNING: CYS 480 has a net charge of -0.1350 !!! WARNING: CYS 483 has a net charge of -0.1350 !!! WARNING: LYS 523 has a net charge of 0.0200 !!! WARNING: ARG 537 has a net charge of 0.0400 !!! WARNING: CYS 608 has a net charge of -0.1350 !!! WARNING: CYS 611 has a net charge of -0.1350 !!! WARNING: CYS 640 has a net charge of -0.1350 !!! WARNING: CYS 643 has a net charge of -0.1350 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: 0.5886730 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): 12.39400 71.63600 ymin,ymax (A): -28.62500 31.85000 zmin,zma (A): 25.69000 81.92700 x,y,z range (A): 59.24200 60.47500 56.23700 scale (grids/A): 0.5886730 object centre (A): 42.01500 1.612500 53.80850 number of atom coordinates read : 5095 total number of charged atoms : 4926 net assigned charge : 13.04100 assigned positive charge : 777.4373 centred at (gu) : 89.55135 90.62330 90.81202 assigned negative charge : -764.4022 centred at (gu) : 89.49854 90.67171 90.90150 start vw surface at 0.2300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 12003 nv = 96 ne = 84 npr = 100565 no. pairs analyzed = 100565 no. exposed pairs = 6488 no. arc points = 43879 no. surface atoms = 2189 nbur = 2906 mkacc time = 0.2800000 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 = 1.456000 m= 539 mr = 6626 m= 4 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 0.3199999 no. cavity mid-points inaccessible to solvent = 29 time to turn everything in is 0.5800000 number of dielectric boundary points 5878 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4411 ## 402 charges are in solution ## iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 14968 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.9364585E-09 -8.1244922E-10 midg,1,midg; midg,igrid,midg 5.4880931E-09 1.6615608E-09 1,midg,midg; igrid,midg,midg 1.3549699E-09 5.9058611E-09 gauss-seidel spectral radius is 0.9852806 estimated iterations to convergence 68 setup time was (sec) 0.8600000 now iterating at: 11:42:41 rms-change max change #iterations 0.1378233 16.39693 at 10iterations 1.2010620E-02 1.335415 at 20iterations 2.0168675E-03 0.1859322 at 30iterations 8.0997072E-04 5.9279442E-02 at 40iterations 3.6884681E-04 2.4398804E-02 at 50iterations finished qdiffx linear iterations at : 11:42:45 total time elapsed so far: 4.200000 # loops : 50 mean,max change (kT/e) : 3.6884681E-04 2.4398804E-02 energy calculations done at 4.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.380000 DelPhi exited at 11:42:45 4.383u 0.267s 0:04.96 93.5% 0+0k 0+0io 6pf+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 Thu Jan 19 2012 at 11:42:45 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5095 !!! WARNING: LYS 37 has a net charge of 0.0200 !!! WARNING: TYR 44 has a net charge of 0.0210 !!! WARNING: ARG 54 has a net charge of 0.0400 !!! WARNING: CYS 125 has a net charge of -0.1350 !!! WARNING: CYS 128 has a net charge of -0.1350 !!! WARNING: CYS 157 has a net charge of -0.1350 !!! WARNING: CYS 160 has a net charge of -0.1350 !!! WARNING: LYS 200 has a net charge of 0.0200 !!! WARNING: ARG 214 has a net charge of 0.0400 !!! WARNING: CYS 285 has a net charge of -0.1350 !!! WARNING: CYS 288 has a net charge of -0.1350 !!! WARNING: CYS 317 has a net charge of -0.1350 !!! WARNING: CYS 320 has a net charge of -0.1350 !!! WARNING: CYS 448 has a net charge of -0.1350 !!! WARNING: CYS 451 has a net charge of -0.1350 !!! WARNING: CYS 480 has a net charge of -0.1350 !!! WARNING: CYS 483 has a net charge of -0.1350 !!! WARNING: LYS 523 has a net charge of 0.0200 !!! WARNING: ARG 537 has a net charge of 0.0400 !!! WARNING: CYS 608 has a net charge of -0.1350 !!! WARNING: CYS 611 has a net charge of -0.1350 !!! WARNING: CYS 640 has a net charge of -0.1350 !!! WARNING: CYS 643 has a net charge of -0.1350 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: 1.766019 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): 12.39400 71.63600 ymin,ymax (A): -28.62500 31.85000 zmin,zma (A): 25.69000 81.92700 x,y,z range (A): 59.24200 60.47500 56.23700 scale (grids/A): 1.766019 object centre (A): 42.01500 1.612500 53.80850 number of atom coordinates read : 5095 total number of charged atoms : 4926 net assigned charge : 13.04100 assigned positive charge : 777.4373 centred at (gu) : 88.65215 91.86835 92.43472 assigned negative charge : -764.4022 centred at (gu) : 88.49532 92.01501 92.70430 start vw surface at 0.2300000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 132231 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43879 grid for indexing accessible points = 1.400000 m= 45702 mr = 93413 m= 5293 mr = 32853 m= 174 mr = 2608 m= 1 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.5900000 no. cavity mid-points inaccessible to solvent = 3609 time to turn everything in is 1.100000 number of dielectric boundary points 54506 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 323 ## 1 charges are in solution ## iepsmp to db, and charging done at 1.260000 number of grid points assigned charge 38244 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) : 0.5886730 object centre at (A) : 42.01500 1.612500 53.80850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.4623221E-02 2.1784622E-03 midg,1,midg; midg,igrid,midg 2.1166725E-02 1.2360248E-02 1,midg,midg; igrid,midg,midg 8.9730553E-02 8.2316995E-02 gauss-seidel spectral radius is 0.9986626 estimated iterations to convergence 217 setup time was (sec) 1.420000 now iterating at: 11:42:48 rms-change max change #iterations 5.476745 220.2565 at 10iterations 2.597915 71.35227 at 20iterations 1.236451 32.21910 at 30iterations 0.5875279 14.27125 at 40iterations 0.2803692 7.450706 at 50iterations 0.1335955 3.349426 at 60iterations 6.3605025E-02 1.800706 at 70iterations 3.0384617E-02 0.8095875 at 80iterations 1.4548639E-02 0.4070587 at 90iterations 7.0543662E-03 0.1690483 at 100iterations 3.4942219E-03 9.0563059E-02 at 110iterations 1.8128217E-03 4.2343140E-02 at 120iterations finished qdiffx linear iterations at : 11:42:57 total time elapsed so far: 10.32000 # loops : 120 mean,max change (kT/e) : 1.8128217E-03 4.2343140E-02 energy calculations done at 10.32000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.50000 DelPhi exited at 11:42:57 10.499u 0.308s 0:11.89 90.7% 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 Thu Jan 19 2012 at 11:42:57 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5095 !!! WARNING: LYS 37 has a net charge of 0.0200 !!! WARNING: TYR 44 has a net charge of 0.0210 !!! WARNING: ARG 54 has a net charge of 0.0400 !!! WARNING: CYS 125 has a net charge of -0.1350 !!! WARNING: CYS 128 has a net charge of -0.1350 !!! WARNING: CYS 157 has a net charge of -0.1350 !!! WARNING: CYS 160 has a net charge of -0.1350 !!! WARNING: LYS 200 has a net charge of 0.0200 !!! WARNING: ARG 214 has a net charge of 0.0400 !!! WARNING: CYS 285 has a net charge of -0.1350 !!! WARNING: CYS 288 has a net charge of -0.1350 !!! WARNING: CYS 317 has a net charge of -0.1350 !!! WARNING: CYS 320 has a net charge of -0.1350 !!! WARNING: CYS 448 has a net charge of -0.1350 !!! WARNING: CYS 451 has a net charge of -0.1350 !!! WARNING: CYS 480 has a net charge of -0.1350 !!! WARNING: CYS 483 has a net charge of -0.1350 !!! WARNING: LYS 523 has a net charge of 0.0200 !!! WARNING: ARG 537 has a net charge of 0.0400 !!! WARNING: CYS 608 has a net charge of -0.1350 !!! WARNING: CYS 611 has a net charge of -0.1350 !!! WARNING: CYS 640 has a net charge of -0.1350 !!! WARNING: CYS 643 has a net charge of -0.1350 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: 2.649029 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): 12.39400 71.63600 ymin,ymax (A): -28.62500 31.85000 zmin,zma (A): 25.69000 81.92700 x,y,z range (A): 59.24200 60.47500 56.23700 scale (grids/A): 2.649029 object centre (A): 42.01500 1.612500 53.80850 number of atom coordinates read : 5095 total number of charged atoms : 4926 net assigned charge : 13.04100 assigned positive charge : 777.4373 centred at (gu) : 87.97785 92.80238 93.65175 assigned negative charge : -764.4022 centred at (gu) : 87.74280 93.02237 94.05641 start vw surface at 0.2400000 fill in re-entrant regions at 0.9100000 boundary points on vw surface= 306129 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43879 grid for indexing accessible points = 1.400000 m= 155093 mr = 226356 m= 48061 mr = 126409 m= 8554 mr = 36680 m= 749 mr = 5614 m= 19 mr = 326 m= 0 mr = 0 ibnd upper bound 518605 exceeds ibmx 16.606u 0.122s 0:16.81 99.4% 0+0k 0+0io 0pf+0w