Sun Oct 9 00:28:00 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 Sun Oct 9 2011 at 00:28:00 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: 317 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2276 !!! WARNING: HIT 84 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: 0.6528636 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): 0.4529999 53.42100 ymin,ymax (A): 8.105000 51.42700 zmin,zma (A): -6.242000 48.28700 x,y,z range (A): 52.96800 43.32200 54.52900 scale (grids/A): 0.6528636 object centre (A): 26.93700 29.76600 21.02250 number of atom coordinates read : 2276 total number of charged atoms : 2142 net assigned charge : 9.514019 assigned positive charge : 333.8766 centred at (gu) : 89.51508 90.91130 89.01704 assigned negative charge : -324.3632 centred at (gu) : 89.51999 90.81018 88.98626 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 6748 nv = 96 ne = 84 npr = 45548 no. pairs analyzed = 45548 no. exposed pairs = 3006 no. arc points = 21859 no. surface atoms = 1008 nbur = 1268 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 367 mr = 3534 m= 1 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2700000 number of dielectric boundary points 3548 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2058 ## 188 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 7824 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8915323E-08 1.9635431E-08 midg,1,midg; midg,igrid,midg 4.9050217E-09 4.0512329E-08 1,midg,midg; igrid,midg,midg 2.2565340E-08 1.7319271E-08 gauss-seidel spectral radius is 0.9878210 estimated iterations to convergence 74 setup time was (sec) 0.5700000 now iterating at: 00:28:01 rms-change max change #iterations 0.1462319 22.06720 at 10iterations 1.4974917E-02 1.993738 at 20iterations 1.5629595E-03 0.2326317 at 30iterations 1.7959898E-04 2.5476456E-02 at 40iterations 2.8235241E-05 5.0868988E-03 at 50iterations finished qdiffx linear iterations at : 00:28:05 total time elapsed so far: 4.280000 # loops : 50 mean,max change (kT/e) : 2.8235241E-05 5.0868988E-03 energy calculations done at 4.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.450000 DelPhi exited at 00:28:05 4.455u 0.408s 0:05.13 94.5% 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 Sun Oct 9 2011 at 00:28:05 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: 317 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2276 !!! WARNING: HIT 84 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: 1.958591 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): 0.4529999 53.42100 ymin,ymax (A): 8.105000 51.42700 zmin,zma (A): -6.242000 48.28700 x,y,z range (A): 52.96800 43.32200 54.52900 scale (grids/A): 1.958591 object centre (A): 26.93700 29.76600 21.02250 number of atom coordinates read : 2276 total number of charged atoms : 2142 net assigned charge : 9.514019 assigned positive charge : 333.8766 centred at (gu) : 88.54504 92.73358 87.05083 assigned negative charge : -324.3632 centred at (gu) : 88.56001 92.43085 86.95885 start vw surface at 0.1100000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 71475 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21859 grid for indexing accessible points = 1.400000 m= 25814 mr = 47753 m= 4285 mr = 18607 m= 280 mr = 2593 m= 5 mr = 98 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5700000 number of dielectric boundary points 32808 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 131 iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 16940 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) : 0.6528636 object centre at (A) : 26.93700 29.76600 21.02250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9497281E-02 5.4638993E-02 midg,1,midg; midg,igrid,midg -4.0687453E-03 3.0909579E-02 1,midg,midg; igrid,midg,midg 5.0963487E-02 4.7854159E-02 gauss-seidel spectral radius is 0.9986836 estimated iterations to convergence 218 setup time was (sec) 0.8600000 now iterating at: 00:28:07 rms-change max change #iterations 4.100167 181.9487 at 10iterations 1.945149 68.07088 at 20iterations 0.9198111 31.36123 at 30iterations 0.4386426 14.12577 at 40iterations 0.2074589 7.697476 at 50iterations 9.8103926E-02 3.203175 at 60iterations 4.6541024E-02 1.508453 at 70iterations 2.2072952E-02 0.7602987 at 80iterations 1.0437479E-02 0.3987694 at 90iterations 4.9958136E-03 0.1730385 at 100iterations 2.3710697E-03 7.2326660E-02 at 110iterations 1.1236651E-03 3.6277771E-02 at 120iterations finished qdiffx linear iterations at : 00:28:16 total time elapsed so far: 10.54000 # loops : 120 mean,max change (kT/e) : 1.1236651E-03 3.6277771E-02 energy calculations done at 10.54000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.71000 DelPhi exited at 00:28:17 10.719u 0.447s 0:11.47 97.2% 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 Sun Oct 9 2011 at 00:28:17 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: 317 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2276 !!! WARNING: HIT 84 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: 2.937886 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): 0.4529999 53.42100 ymin,ymax (A): 8.105000 51.42700 zmin,zma (A): -6.242000 48.28700 x,y,z range (A): 52.96800 43.32200 54.52900 scale (grids/A): 2.937886 object centre (A): 26.93700 29.76600 21.02250 number of atom coordinates read : 2276 total number of charged atoms : 2142 net assigned charge : 9.514019 assigned positive charge : 333.8766 centred at (gu) : 87.81750 94.10035 85.57622 assigned negative charge : -324.3632 centred at (gu) : 87.84010 93.64622 85.43829 start vw surface at 0.1100000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 164853 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21859 grid for indexing accessible points = 1.400000 m= 82492 mr = 116274 m= 30803 mr = 65999 m= 7665 mr = 24314 m= 1211 mr = 5644 m= 82 mr = 828 m= 5 mr = 22 m= 0 mr = 0 time to grow re-entrant surface = 0.9300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.540000 number of dielectric boundary points 74030 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.660000 number of grid points assigned charge 17136 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) : 1.958591 object centre at (A) : 26.93700 29.76600 21.02250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2622018 0.7745678 midg,1,midg; midg,igrid,midg -2.2716487E-02 0.2814767 1,midg,midg; igrid,midg,midg 0.4497692 0.5459243 gauss-seidel spectral radius is 0.9992789 estimated iterations to convergence 294 setup time was (sec) 1.870000 now iterating at: 00:28:19 rms-change max change #iterations 9.683909 413.9282 at 10iterations 5.740691 136.9484 at 20iterations 3.398597 80.42735 at 30iterations 1.998718 42.54136 at 40iterations 1.169538 23.31748 at 50iterations 0.6829089 14.54618 at 60iterations 0.3990759 9.356641 at 70iterations 0.2316924 4.507515 at 80iterations 0.1350956 2.570766 at 90iterations 7.8143761E-02 1.365376 at 100iterations 4.5468543E-02 0.9126396 at 110iterations 2.6401671E-02 0.4895515 at 120iterations 1.5281044E-02 0.2867584 at 130iterations 8.8637723E-03 0.1675949 at 140iterations 5.1291822E-03 9.9347115E-02 at 150iterations 2.9700901E-03 5.7757378E-02 at 160iterations 1.7243489E-03 3.0942917E-02 at 170iterations 9.9685160E-04 1.8569946E-02 at 180iterations finished qdiffx linear iterations at : 00:28:35 total time elapsed so far: 17.92000 # loops : 180 mean,max change (kT/e) : 9.9685160E-04 1.8569946E-02 energy calculations done at 17.92000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.08000 DelPhi exited at 00:28:36 18.083u 0.475s 0:18.85 98.4% 0+0k 0+0io 0pf+0w