Sat Oct 8 19:32:52 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 Sat Oct 8 2011 at 19:32:52 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2606 !!! WARNING: HIY 36 has a net charge of 0.2000 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! 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: ZN4 443 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: 0.7038494 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): -5.822000 43.78000 ymin,ymax (A): -3.035000 47.54400 zmin,zma (A): -8.311000 40.47800 x,y,z range (A): 49.60200 50.57900 48.78900 scale (grids/A): 0.7038494 object centre (A): 18.97900 22.25450 16.08350 number of atom coordinates read : 2606 total number of charged atoms : 2462 net assigned charge : 4.106009 assigned positive charge : 393.8351 centred at (gu) : 88.44898 92.04340 90.60981 assigned negative charge : -389.7296 centred at (gu) : 88.31944 92.14011 90.55529 start vw surface at 0.1600000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 8786 nv = 96 ne = 84 npr = 54553 no. pairs analyzed = 54553 no. exposed pairs = 3021 no. arc points = 21579 no. surface atoms = 1011 nbur = 1595 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 605 mr = 5123 m= 4 mr = 141 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 266 time to turn everything in is 0.3100000 number of dielectric boundary points 4131 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2040 ## 176 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 9826 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.8668874E-09 7.2835661E-08 midg,1,midg; midg,igrid,midg 5.9317948E-08 -3.3320003E-08 1,midg,midg; igrid,midg,midg -5.5865243E-08 7.8538712E-08 gauss-seidel spectral radius is 0.9895312 estimated iterations to convergence 80 setup time was (sec) 0.5300000 now iterating at: 19:32:53 rms-change max change #iterations 0.2241964 37.54850 at 10iterations 2.7624015E-02 3.718967 at 20iterations 3.4037607E-03 0.4769650 at 30iterations 4.1120144E-04 6.2300682E-02 at 40iterations 5.0887164E-05 6.4363480E-03 at 50iterations finished qdiffx linear iterations at : 19:32:55 total time elapsed so far: 3.100000 # loops : 50 mean,max change (kT/e) : 5.0887164E-05 6.4363480E-03 energy calculations done at 3.100000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.270000 DelPhi exited at 19:32:56 3.278u 0.215s 0:03.77 92.3% 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 Sat Oct 8 2011 at 19:32:56 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2606 !!! WARNING: HIY 36 has a net charge of 0.2000 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! 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: ZN4 443 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: 2.111548 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): -5.822000 43.78000 ymin,ymax (A): -3.035000 47.54400 zmin,zma (A): -8.311000 40.47800 x,y,z range (A): 49.60200 50.57900 48.78900 scale (grids/A): 2.111548 object centre (A): 18.97900 22.25450 16.08350 number of atom coordinates read : 2606 total number of charged atoms : 2462 net assigned charge : 4.106009 assigned positive charge : 393.8351 centred at (gu) : 85.34650 96.13000 91.82903 assigned negative charge : -389.7296 centred at (gu) : 84.95819 96.42016 91.66557 start vw surface at 0.1500000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 92525 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21579 grid for indexing accessible points = 1.400000 m= 37794 mr = 65676 m= 8024 mr = 29495 m= 768 mr = 5714 m= 12 mr = 399 m= 0 mr = 2 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 8419 time to turn everything in is 0.6500000 number of dielectric boundary points 37837 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 70 iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 19532 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) : 0.7038494 object centre at (A) : 18.97900 22.25450 16.08350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.2724739E-03 1.8993057E-02 midg,1,midg; midg,igrid,midg 8.8169649E-03 -2.3644639E-02 1,midg,midg; igrid,midg,midg -1.1873909E-02 9.8728560E-02 gauss-seidel spectral radius is 0.9988685 estimated iterations to convergence 235 setup time was (sec) 0.9400000 now iterating at: 19:32:57 rms-change max change #iterations 5.226873 208.7011 at 10iterations 2.592995 89.00912 at 20iterations 1.301126 40.14546 at 30iterations 0.6517018 16.90961 at 40iterations 0.3271234 9.303610 at 50iterations 0.1637429 4.251893 at 60iterations 8.2243517E-02 2.566557 at 70iterations 4.1253779E-02 1.093719 at 80iterations 2.0676233E-02 0.5670190 at 90iterations 1.0355010E-02 0.2895279 at 100iterations 5.2043721E-03 0.1507607 at 110iterations 2.6072285E-03 6.9032669E-02 at 120iterations finished qdiffx linear iterations at : 19:33:04 total time elapsed so far: 8.280000 # loops : 120 mean,max change (kT/e) : 2.6072285E-03 6.9032669E-02 energy calculations done at 8.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.460000 DelPhi exited at 19:33:05 8.459u 0.223s 0:08.94 96.9% 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 Sat Oct 8 2011 at 19:33:05 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2606 !!! WARNING: HIY 36 has a net charge of 0.2000 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! 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: ZN4 443 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: 3.167322 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): -5.822000 43.78000 ymin,ymax (A): -3.035000 47.54400 zmin,zma (A): -8.311000 40.47800 x,y,z range (A): 49.60200 50.57900 48.78900 scale (grids/A): 3.167322 object centre (A): 18.97900 22.25450 16.08350 number of atom coordinates read : 2606 total number of charged atoms : 2462 net assigned charge : 4.106009 assigned positive charge : 393.8351 centred at (gu) : 83.01959 99.19485 92.74337 assigned negative charge : -389.7296 centred at (gu) : 82.43725 99.63013 92.49828 start vw surface at 0.1500000 fill in re-entrant regions at 0.9600000 boundary points on vw surface= 213261 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21579 grid for indexing accessible points = 1.400000 m= 116550 mr = 157891 m= 49816 mr = 98444 m= 15359 mr = 41936 m= 3418 mr = 12454 m= 407 mr = 2618 m= 16 mr = 272 m= 0 mr = 3 time to grow re-entrant surface = 1.010000 no. cavity mid-points inaccessible to solvent = 28071 time to turn everything in is 2.110000 number of dielectric boundary points 85209 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.260000 number of grid points assigned charge 19696 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) : 2.111548 object centre at (A) : 18.97900 22.25450 16.08350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2973938 0.1633985 midg,1,midg; midg,igrid,midg 1.8906046E-02 -0.1982663 1,midg,midg; igrid,midg,midg -0.1605552 1.417005 gauss-seidel spectral radius is 0.9993131 estimated iterations to convergence 301 setup time was (sec) 2.430000 now iterating at: 19:33:08 rms-change max change #iterations 11.44655 328.4024 at 10iterations 6.715803 117.1504 at 20iterations 3.954117 64.23432 at 30iterations 2.316353 36.55865 at 40iterations 1.363799 22.01812 at 50iterations 0.7999538 12.17337 at 60iterations 0.4696487 8.037252 at 70iterations 0.2757238 4.481095 at 80iterations 0.1614356 2.495506 at 90iterations 9.4609007E-02 1.428020 at 100iterations 5.5587620E-02 1.023184 at 110iterations 3.2522399E-02 0.5212708 at 120iterations 1.9114044E-02 0.3240662 at 130iterations 1.1210885E-02 0.1805124 at 140iterations 6.5815691E-03 0.1130857 at 150iterations 3.8496014E-03 6.9230556E-02 at 160iterations 2.2614771E-03 3.5121918E-02 at 170iterations 1.3244712E-03 2.0594597E-02 at 180iterations finished qdiffx linear iterations at : 19:33:18 total time elapsed so far: 13.03000 # loops : 180 mean,max change (kT/e) : 1.3244712E-03 2.0594597E-02 energy calculations done at 13.03000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.22000 DelPhi exited at 19:33:19 13.219u 0.214s 0:13.76 97.5% 0+0k 0+0io 0pf+0w