Sat Oct 8 21:02:19 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 21:02:19 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2564 !!! 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 470 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6161621 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): -31.44500 17.39600 ymin,ymax (A): -23.29500 23.32600 zmin,zma (A): -12.50300 45.27400 x,y,z range (A): 48.84100 46.62100 57.77700 scale (grids/A): 0.6161621 object centre (A): -7.024500 1.5500069E-02 16.38550 number of atom coordinates read : 2564 total number of charged atoms : 2462 net assigned charge : 5.000009 assigned positive charge : 393.4760 centred at (gu) : 88.44152 89.02130 89.71139 assigned negative charge : -388.4765 centred at (gu) : 88.37080 89.07118 89.54464 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6347 nv = 96 ne = 84 npr = 52418 no. pairs analyzed = 52418 no. exposed pairs = 3043 no. arc points = 21818 no. surface atoms = 1020 nbur = 1544 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 342 mr = 3497 m= 3 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 34 time to turn everything in is 0.3200000 number of dielectric boundary points 3159 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2154 ## 222 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 7974 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.8665167E-09 1.2516894E-08 midg,1,midg; midg,igrid,midg 8.1764666E-09 5.7639249E-10 1,midg,midg; igrid,midg,midg -9.1559188E-10 5.5546416E-09 gauss-seidel spectral radius is 0.9863547 estimated iterations to convergence 70 setup time was (sec) 0.6200000 now iterating at: 21:02:20 rms-change max change #iterations 0.1217236 19.23551 at 10iterations 1.1079891E-02 1.692883 at 20iterations 1.0216293E-03 0.1525955 at 30iterations 9.7442316E-05 1.5111923E-02 at 40iterations 9.6006106E-06 1.5926361E-03 at 50iterations finished qdiffx linear iterations at : 21:02:24 total time elapsed so far: 4.370000 # loops : 50 mean,max change (kT/e) : 9.6006106E-06 1.5926361E-03 energy calculations done at 4.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.540000 DelPhi exited at 21:02:24 4.548u 0.407s 0:05.21 94.8% 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 21:02:24 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2564 !!! 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 470 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.848486 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): -31.44500 17.39600 ymin,ymax (A): -23.29500 23.32600 zmin,zma (A): -12.50300 45.27400 x,y,z range (A): 48.84100 46.62100 57.77700 scale (grids/A): 1.848486 object centre (A): -7.024500 1.5500069E-02 16.38550 number of atom coordinates read : 2564 total number of charged atoms : 2462 net assigned charge : 5.000009 assigned positive charge : 393.4760 centred at (gu) : 85.32396 87.06368 89.13364 assigned negative charge : -388.4765 centred at (gu) : 85.11205 87.21357 88.63371 start vw surface at 0.1200000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 69729 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21818 grid for indexing accessible points = 1.400000 m= 23816 mr = 48577 m= 3252 mr = 17473 m= 131 mr = 1853 m= 2 mr = 29 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 2635 time to turn everything in is 0.5600000 number of dielectric boundary points 28998 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 185 iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 19327 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) : 0.6161621 object centre at (A) : -7.024500 1.5500069E-02 16.38550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.0658704E-02 3.0571636E-02 midg,1,midg; midg,igrid,midg 1.3051103E-02 1.4856195E-03 1,midg,midg; igrid,midg,midg 1.9131856E-03 2.8486172E-02 gauss-seidel spectral radius is 0.9985465 estimated iterations to convergence 208 setup time was (sec) 0.8800000 now iterating at: 21:02:26 rms-change max change #iterations 3.979177 209.5644 at 10iterations 1.812543 64.52393 at 20iterations 0.8252898 26.26895 at 30iterations 0.3780104 12.98554 at 40iterations 0.1729810 5.615482 at 50iterations 7.9160385E-02 2.605624 at 60iterations 3.6147028E-02 1.136063 at 70iterations 1.6593762E-02 0.6009588 at 80iterations 7.5697093E-03 0.2414322 at 90iterations 3.4489587E-03 0.1175385 at 100iterations 1.5855456E-03 5.6432724E-02 at 110iterations 7.2389178E-04 2.5026321E-02 at 120iterations finished qdiffx linear iterations at : 21:02:35 total time elapsed so far: 10.59000 # loops : 120 mean,max change (kT/e) : 7.2389178E-04 2.5026321E-02 energy calculations done at 10.59000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.75000 DelPhi exited at 21:02:36 10.758u 0.440s 0:11.47 97.5% 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 Sat Oct 8 2011 at 21:02:36 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2564 !!! 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 470 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.772730 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): -31.44500 17.39600 ymin,ymax (A): -23.29500 23.32600 zmin,zma (A): -12.50300 45.27400 x,y,z range (A): 48.84100 46.62100 57.77700 scale (grids/A): 2.772730 object centre (A): -7.024500 1.5500069E-02 16.38550 number of atom coordinates read : 2564 total number of charged atoms : 2462 net assigned charge : 5.000009 assigned positive charge : 393.4760 centred at (gu) : 82.98583 85.59541 88.70040 assigned negative charge : -388.4765 centred at (gu) : 82.66805 85.82033 87.95033 start vw surface at 0.1200000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 161538 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21818 grid for indexing accessible points = 1.400000 m= 79245 mr = 117865 m= 26481 mr = 64883 m= 5728 mr = 21021 m= 621 mr = 4102 m= 27 mr = 334 m= 0 mr = 8 time to grow re-entrant surface = 0.8600000 no. cavity mid-points inaccessible to solvent = 8690 time to turn everything in is 1.450000 number of dielectric boundary points 65427 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.580000 number of grid points assigned charge 19694 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) : 1.848486 object centre at (A) : -7.024500 1.5500069E-02 16.38550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1250610 0.2970180 midg,1,midg; midg,igrid,midg 0.1426239 -8.7724376E-04 1,midg,midg; igrid,midg,midg 1.2047051E-02 0.3922442 gauss-seidel spectral radius is 0.9992288 estimated iterations to convergence 284 setup time was (sec) 1.770000 now iterating at: 21:02:38 rms-change max change #iterations 9.465522 283.1815 at 10iterations 5.444424 139.4382 at 20iterations 3.110773 83.35291 at 30iterations 1.776091 38.35512 at 40iterations 1.010777 23.79177 at 50iterations 0.5761669 11.00948 at 60iterations 0.3277827 6.827063 at 70iterations 0.1863973 3.863714 at 80iterations 0.1056957 2.048954 at 90iterations 6.0111016E-02 1.108453 at 100iterations 3.4145083E-02 0.6352749 at 110iterations 1.9385798E-02 0.4151649 at 120iterations 1.1006229E-02 0.2247972 at 130iterations 6.2666670E-03 0.1245651 at 140iterations 3.5474524E-03 7.4193954E-02 at 150iterations 2.0130121E-03 3.7342072E-02 at 160iterations 1.1486711E-03 2.2941589E-02 at 170iterations 6.5238791E-04 1.2287140E-02 at 180iterations finished qdiffx linear iterations at : 21:02:54 total time elapsed so far: 17.81000 # loops : 180 mean,max change (kT/e) : 6.5238791E-04 1.2287140E-02 energy calculations done at 17.81000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.98000 DelPhi exited at 21:02:54 17.983u 0.469s 0:18.71 98.5% 0+0k 0+0io 0pf+0w