Wed Dec 28 11:01:58 PST 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 Wed Dec 28 2011 at 11:01:58 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1966 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: 0.6231947 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): -35.11300 10.02100 ymin,ymax (A): 1.131000 41.16700 zmin,zma (A): -1.747000 55.37800 x,y,z range (A): 45.13400 40.03600 57.12500 scale (grids/A): 0.6231947 object centre (A): -12.54600 21.14900 26.81550 number of atom coordinates read : 1966 total number of charged atoms : 1834 net assigned charge : 4.000004 assigned positive charge : 287.8720 centred at (gu) : 90.37812 89.64185 90.65070 assigned negative charge : -283.8723 centred at (gu) : 90.33180 89.73444 90.67663 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 5201 nv = 96 ne = 84 npr = 40662 no. pairs analyzed = 40662 no. exposed pairs = 2479 no. arc points = 17061 no. surface atoms = 840 nbur = 1126 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 246 mr = 2891 m= 0 mr = 26 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2700000 number of dielectric boundary points 2530 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1693 ## 164 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 6134 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.2706869E-09 2.4494107E-09 midg,1,midg; midg,igrid,midg 9.1036236E-09 -1.3317573E-09 1,midg,midg; igrid,midg,midg 9.7804131E-10 6.4997479E-09 gauss-seidel spectral radius is 0.9866084 estimated iterations to convergence 71 setup time was (sec) 0.7300000 now iterating at: 11:02:00 rms-change max change #iterations 0.1086014 18.87814 at 10iterations 9.8825609E-03 1.524307 at 20iterations 9.2792918E-04 0.1805115 at 30iterations 8.5030391E-05 1.3076782E-02 at 40iterations 7.9461388E-06 1.2054443E-03 at 50iterations finished qdiffx linear iterations at : 11:02:05 total time elapsed so far: 5.980000 # loops : 50 mean,max change (kT/e) : 7.9461388E-06 1.2054443E-03 energy calculations done at 5.980000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.150000 DelPhi exited at 11:02:08 6.156u 0.764s 0:09.46 73.0% 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 Wed Dec 28 2011 at 11:02:09 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1966 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.869584 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): -35.11300 10.02100 ymin,ymax (A): 1.131000 41.16700 zmin,zma (A): -1.747000 55.37800 x,y,z range (A): 45.13400 40.03600 57.12500 scale (grids/A): 1.869584 object centre (A): -12.54600 21.14900 26.81550 number of atom coordinates read : 1966 total number of charged atoms : 1834 net assigned charge : 4.000004 assigned positive charge : 287.8720 centred at (gu) : 91.13432 88.92574 91.95223 assigned negative charge : -283.8723 centred at (gu) : 90.99554 89.20344 92.03011 start vw surface at 0.1100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 55780 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17061 grid for indexing accessible points = 1.400000 m= 20148 mr = 38587 m= 2828 mr = 15214 m= 138 mr = 1778 m= 2 mr = 67 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 230 time to turn everything in is 0.5600000 number of dielectric boundary points 23250 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 122 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 14383 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) : 0.6231947 object centre at (A) : -12.54600 21.14900 26.81550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.5886279E-02 3.6642596E-02 midg,1,midg; midg,igrid,midg 3.4574769E-03 -1.8100990E-03 1,midg,midg; igrid,midg,midg -1.3001241E-03 -1.1687051E-03 gauss-seidel spectral radius is 0.9985064 estimated iterations to convergence 205 setup time was (sec) 1.120000 now iterating at: 11:02:11 rms-change max change #iterations 3.427227 164.0930 at 10iterations 1.555078 60.89600 at 20iterations 0.7015363 25.02482 at 30iterations 0.3172091 11.54693 at 40iterations 0.1434013 5.087682 at 50iterations 6.4838022E-02 2.283501 at 60iterations 2.9364362E-02 1.136741 at 70iterations 1.3244041E-02 0.5344172 at 80iterations 5.9823291E-03 0.2256618 at 90iterations 2.7200209E-03 0.1055565 at 100iterations 1.2250145E-03 4.6046734E-02 at 110iterations 5.5520888E-04 1.9683838E-02 at 120iterations finished qdiffx linear iterations at : 11:02:28 total time elapsed so far: 17.92000 # loops : 120 mean,max change (kT/e) : 5.5520888E-04 1.9683838E-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) 18.09000 DelPhi exited at 11:02:29 18.092u 0.829s 0:19.89 95.0% 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 Wed Dec 28 2011 at 11:02:30 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1966 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: 2.804376 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): -35.11300 10.02100 ymin,ymax (A): 1.131000 41.16700 zmin,zma (A): -1.747000 55.37800 x,y,z range (A): 45.13400 40.03600 57.12500 scale (grids/A): 2.804376 object centre (A): -12.54600 21.14900 26.81550 number of atom coordinates read : 1966 total number of charged atoms : 1834 net assigned charge : 4.000004 assigned positive charge : 287.8720 centred at (gu) : 91.70150 88.38856 92.92829 assigned negative charge : -283.8723 centred at (gu) : 91.49329 88.80517 93.04514 start vw surface at 0.1100000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 128823 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17061 grid for indexing accessible points = 1.400000 m= 65845 mr = 93403 m= 23117 mr = 54451 m= 5026 mr = 18958 m= 579 mr = 3801 m= 32 mr = 422 m= 0 mr = 11 time to grow re-entrant surface = 0.8100001 no. cavity mid-points inaccessible to solvent = 911 time to turn everything in is 1.390000 number of dielectric boundary points 52376 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.620000 number of grid points assigned charge 14671 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) : 1.869584 object centre at (A) : -12.54600 21.14900 26.81550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1507533 0.3345134 midg,1,midg; midg,igrid,midg -2.2666203E-02 -1.8156510E-02 1,midg,midg; igrid,midg,midg -5.4117709E-02 -5.5613179E-02 gauss-seidel spectral radius is 0.9992049 estimated iterations to convergence 280 setup time was (sec) 1.960000 now iterating at: 11:02:32 rms-change max change #iterations 8.164551 342.5205 at 10iterations 4.684389 142.8004 at 20iterations 2.660763 66.52571 at 30iterations 1.504257 32.76244 at 40iterations 0.8481428 19.08356 at 50iterations 0.4785147 9.753078 at 60iterations 0.2701135 5.729001 at 70iterations 0.1517572 3.558430 at 80iterations 8.5700095E-02 1.765554 at 90iterations 4.8112102E-02 1.012308 at 100iterations 2.7046941E-02 0.5446219 at 110iterations 1.5241072E-02 0.3225956 at 120iterations 8.5409908E-03 0.1799622 at 130iterations 4.8033684E-03 0.1004874 at 140iterations 2.6984194E-03 5.5598736E-02 at 150iterations 1.5186323E-03 3.3063889E-02 at 160iterations 8.5320795E-04 1.8270493E-02 at 170iterations 4.8020150E-04 9.6321106E-03 at 180iterations finished qdiffx linear iterations at : 11:03:00 total time elapsed so far: 29.48000 # loops : 180 mean,max change (kT/e) : 4.8020150E-04 9.6321106E-03 energy calculations done at 29.48000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 29.66000 DelPhi exited at 11:03:02 29.662u 0.854s 0:32.22 94.6% 0+0k 0+0io 0pf+0w