Mon Oct 10 14:03:16 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 14:03:16 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2576 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN6 640 has a net charge of 1.4000 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: 0.6149912 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): -32.47900 17.65800 ymin,ymax (A): -23.59500 23.49500 zmin,zma (A): -12.46700 45.42000 x,y,z range (A): 50.13700 47.09000 57.88700 scale (grids/A): 0.6149912 object centre (A): -7.410500 -5.0000191E-02 16.47650 number of atom coordinates read : 2576 total number of charged atoms : 2455 net assigned charge : 3.000009 assigned positive charge : 393.4890 centred at (gu) : 88.77239 89.14127 89.59624 assigned negative charge : -390.4895 centred at (gu) : 88.68616 89.19244 89.50162 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6299 nv = 96 ne = 84 npr = 53624 no. pairs analyzed = 53624 no. exposed pairs = 2963 no. arc points = 21572 no. surface atoms = 997 nbur = 1579 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 300 mr = 3503 m= 1 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 100 time to turn everything in is 0.2800000 number of dielectric boundary points 3069 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2168 ## 226 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 7980 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.7099017E-09 6.8834485E-09 midg,1,midg; midg,igrid,midg 6.1344196E-09 -6.6667322E-10 1,midg,midg; igrid,midg,midg -3.8529016E-09 5.3793956E-09 gauss-seidel spectral radius is 0.9863027 estimated iterations to convergence 70 setup time was (sec) 0.5100000 now iterating at: 14:03:17 rms-change max change #iterations 0.1221296 17.91389 at 10iterations 1.1183401E-02 1.674049 at 20iterations 9.7958778E-04 0.1536322 at 30iterations 8.8452827E-05 1.2643814E-02 at 40iterations 8.1332737E-06 1.2102127E-03 at 50iterations finished qdiffx linear iterations at : 14:03:20 total time elapsed so far: 3.110000 # loops : 50 mean,max change (kT/e) : 8.1332737E-06 1.2102127E-03 energy calculations done at 3.110000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.310000 DelPhi exited at 14:03:20 3.313u 0.194s 0:04.01 87.2% 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 14:03:20 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2576 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN6 640 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.844974 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): -32.47900 17.65800 ymin,ymax (A): -23.59500 23.49500 zmin,zma (A): -12.46700 45.42000 x,y,z range (A): 50.13700 47.09000 57.88700 scale (grids/A): 1.844974 object centre (A): -7.410500 -5.0000191E-02 16.47650 number of atom coordinates read : 2576 total number of charged atoms : 2455 net assigned charge : 3.000009 assigned positive charge : 393.4890 centred at (gu) : 86.31696 87.42349 88.78837 assigned negative charge : -390.4895 centred at (gu) : 86.05827 87.57689 88.50455 start vw surface at 0.1600000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 69410 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21572 grid for indexing accessible points = 1.400000 m= 23601 mr = 48632 m= 3216 mr = 17515 m= 136 mr = 1944 m= 0 mr = 45 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 4474 time to turn everything in is 0.5000000 number of dielectric boundary points 28227 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 176 iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 19217 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) : 0.6149912 object centre at (A) : -7.410500 -5.0000191E-02 16.47650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3925348E-02 2.0199370E-02 midg,1,midg; midg,igrid,midg 1.2926900E-02 4.0843195E-05 1,midg,midg; igrid,midg,midg -4.9815187E-03 2.5483806E-02 gauss-seidel spectral radius is 0.9985420 estimated iterations to convergence 208 setup time was (sec) 0.7800000 now iterating at: 14:03:21 rms-change max change #iterations 3.977201 162.7634 at 10iterations 1.815832 72.68798 at 20iterations 0.8284131 30.11599 at 30iterations 0.3794720 12.92048 at 40iterations 0.1732963 6.238367 at 50iterations 7.9410911E-02 2.538853 at 60iterations 3.6234282E-02 1.290915 at 70iterations 1.6504133E-02 0.5452657 at 80iterations 7.5404681E-03 0.2468929 at 90iterations 3.4380776E-03 0.1166458 at 100iterations 1.5758524E-03 5.4937363E-02 at 110iterations 7.2140974E-04 2.4551392E-02 at 120iterations finished qdiffx linear iterations at : 14:03:28 total time elapsed so far: 7.250000 # loops : 120 mean,max change (kT/e) : 7.2140974E-04 2.4551392E-02 energy calculations done at 7.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.450000 DelPhi exited at 14:03:28 7.453u 0.207s 0:08.03 95.2% 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 14:03:29 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2576 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN6 640 has a net charge of 1.4000 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: 2.767461 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): -32.47900 17.65800 ymin,ymax (A): -23.59500 23.49500 zmin,zma (A): -12.46700 45.42000 x,y,z range (A): 50.13700 47.09000 57.88700 scale (grids/A): 2.767461 object centre (A): -7.410500 -5.0000191E-02 16.47650 number of atom coordinates read : 2576 total number of charged atoms : 2455 net assigned charge : 3.000009 assigned positive charge : 393.4890 centred at (gu) : 84.47531 86.13511 88.18238 assigned negative charge : -390.4895 centred at (gu) : 84.08741 86.36534 87.75668 start vw surface at 0.1600000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 160638 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21572 grid for indexing accessible points = 1.400000 m= 78944 mr = 117769 m= 26171 mr = 65013 m= 5739 mr = 21077 m= 689 mr = 4313 m= 20 mr = 461 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.6600001 no. cavity mid-points inaccessible to solvent = 14473 time to turn everything in is 1.210000 number of dielectric boundary points 63566 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.350000 number of grid points assigned charge 19639 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) : 1.844974 object centre at (A) : -7.410500 -5.0000191E-02 16.47650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.5612039E-02 0.2884042 midg,1,midg; midg,igrid,midg 0.1553757 -1.6026715E-02 1,midg,midg; igrid,midg,midg -3.4885384E-02 0.3544335 gauss-seidel spectral radius is 0.9992270 estimated iterations to convergence 284 setup time was (sec) 1.530000 now iterating at: 14:03:30 rms-change max change #iterations 9.442965 267.2242 at 10iterations 5.400369 138.4574 at 20iterations 3.065750 75.16431 at 30iterations 1.746471 39.43269 at 40iterations 0.9902645 20.50965 at 50iterations 0.5634845 11.62530 at 60iterations 0.3200642 6.682068 at 70iterations 0.1814461 3.773374 at 80iterations 0.1028035 2.041367 at 90iterations 5.8318660E-02 1.102747 at 100iterations 3.3117957E-02 0.6222839 at 110iterations 1.8769041E-02 0.3656507 at 120iterations 1.0637593E-02 0.2197466 at 130iterations 6.0384250E-03 0.1202242 at 140iterations 3.4229262E-03 6.6919327E-02 at 150iterations 1.9390030E-03 3.5364151E-02 at 160iterations 1.0978323E-03 2.1439552E-02 at 170iterations 6.2304031E-04 1.2882233E-02 at 180iterations finished qdiffx linear iterations at : 14:03:41 total time elapsed so far: 11.87000 # loops : 180 mean,max change (kT/e) : 6.2304031E-04 1.2882233E-02 energy calculations done at 11.87000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.05000 DelPhi exited at 14:03:41 12.057u 0.237s 0:12.74 96.3% 0+0k 0+0io 0pf+0w