Mon Oct 10 17:00:57 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 17:00:57 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3445 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: 0.6430520 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): 12.22500 62.72800 ymin,ymax (A): -41.70100 10.44000 zmin,zma (A): 30.13500 85.49600 x,y,z range (A): 50.50300 52.14100 55.36100 scale (grids/A): 0.6430520 object centre (A): 37.47650 -15.63050 57.81550 number of atom coordinates read : 3445 total number of charged atoms : 3297 net assigned charge : 3.000040 assigned positive charge : 529.3494 centred at (gu) : 89.30933 91.01056 89.48336 assigned negative charge : -526.3506 centred at (gu) : 89.34216 90.96652 89.54846 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 9455 nv = 96 ne = 84 npr = 71262 no. pairs analyzed = 71262 no. exposed pairs = 3743 no. arc points = 25972 no. surface atoms = 1263 nbur = 2182 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 543 mr = 5709 m= 3 mr = 75 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 71 time to turn everything in is 0.2600000 number of dielectric boundary points 4217 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2627 ## 248 charges are in solution ## iepsmp to db, and charging done at 0.3300000 number of grid points assigned charge 11506 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.7499959E-08 -5.9507630E-09 midg,1,midg; midg,igrid,midg -2.3868161E-09 1.5011821E-08 1,midg,midg; igrid,midg,midg 1.1797693E-08 -9.0297858E-10 gauss-seidel spectral radius is 0.9875329 estimated iterations to convergence 73 setup time was (sec) 0.4700000 now iterating at: 17:00:58 rms-change max change #iterations 0.1765855 22.52394 at 10iterations 1.8249558E-02 2.351489 at 20iterations 2.0888296E-03 0.2667313 at 30iterations 4.5285781E-04 4.6819687E-02 at 40iterations 1.7463416E-04 1.9569397E-02 at 50iterations finished qdiffx linear iterations at : 17:01:01 total time elapsed so far: 3.340000 # loops : 50 mean,max change (kT/e) : 1.7463416E-04 1.9569397E-02 energy calculations done at 3.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.480000 DelPhi exited at 17:01:02 3.479u 0.202s 0:04.96 73.9% 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 Mon Oct 10 2011 at 17:01:02 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3445 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: 1.929156 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): 12.22500 62.72800 ymin,ymax (A): -41.70100 10.44000 zmin,zma (A): 30.13500 85.49600 x,y,z range (A): 50.50300 52.14100 55.36100 scale (grids/A): 1.929156 object centre (A): 37.47650 -15.63050 57.81550 number of atom coordinates read : 3445 total number of charged atoms : 3297 net assigned charge : 3.000040 assigned positive charge : 529.3494 centred at (gu) : 87.92712 93.03094 88.44926 assigned negative charge : -526.3506 centred at (gu) : 88.02600 92.89906 88.64486 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 102302 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25972 grid for indexing accessible points = 1.400000 m= 40033 mr = 75302 m= 6707 mr = 30952 m= 460 mr = 4336 m= 5 mr = 202 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 2229 time to turn everything in is 0.4700000 number of dielectric boundary points 38715 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 129 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 25939 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) : 0.6430520 object centre at (A) : 37.47650 -15.63050 57.81550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.3068290E-02 -1.4255549E-02 midg,1,midg; midg,igrid,midg -8.0675986E-03 2.8794270E-02 1,midg,midg; igrid,midg,midg 2.4009652E-02 4.1787341E-02 gauss-seidel spectral radius is 0.9987344 estimated iterations to convergence 223 setup time was (sec) 0.6900000 now iterating at: 17:01:03 rms-change max change #iterations 5.192806 175.4424 at 10iterations 2.518147 78.80344 at 20iterations 1.218450 34.62922 at 30iterations 0.5903645 16.56335 at 40iterations 0.2855661 9.112153 at 50iterations 0.1380370 3.909889 at 60iterations 6.6998109E-02 1.835083 at 70iterations 3.2449540E-02 0.8747513 at 80iterations 1.5732421E-02 0.4149218 at 90iterations 7.7019539E-03 0.2000268 at 100iterations 3.8047524E-03 0.1038132 at 110iterations 1.9405725E-03 5.2949905E-02 at 120iterations finished qdiffx linear iterations at : 17:01:10 total time elapsed so far: 7.820000 # loops : 120 mean,max change (kT/e) : 1.9405725E-03 5.2949905E-02 energy calculations done at 7.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.950000 DelPhi exited at 17:01:12 7.951u 0.225s 0:09.77 83.6% 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 17:01:12 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3445 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: 2.893734 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): 12.22500 62.72800 ymin,ymax (A): -41.70100 10.44000 zmin,zma (A): 30.13500 85.49600 x,y,z range (A): 50.50300 52.14100 55.36100 scale (grids/A): 2.893734 object centre (A): 37.47650 -15.63050 57.81550 number of atom coordinates read : 3445 total number of charged atoms : 3297 net assigned charge : 3.000040 assigned positive charge : 529.3494 centred at (gu) : 86.89037 94.54611 87.67361 assigned negative charge : -526.3506 centred at (gu) : 87.03879 94.34852 87.96714 start vw surface at 0.1000000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 236420 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25972 grid for indexing accessible points = 1.400000 m= 128220 mr = 180929 m= 48569 mr = 108359 m= 12206 mr = 40143 m= 1957 mr = 9288 m= 165 mr = 1350 m= 2 mr = 98 m= 0 mr = 0 time to grow re-entrant surface = 0.7600000 no. cavity mid-points inaccessible to solvent = 7567 time to turn everything in is 1.290000 number of dielectric boundary points 87372 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.380000 number of grid points assigned charge 26376 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) : 1.929156 object centre at (A) : 37.47650 -15.63050 57.81550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4310061 -3.8720477E-02 midg,1,midg; midg,igrid,midg -5.3167135E-02 0.3766265 1,midg,midg; igrid,midg,midg 0.3009669 0.5407849 gauss-seidel spectral radius is 0.9992919 estimated iterations to convergence 297 setup time was (sec) 1.530000 now iterating at: 17:01:14 rms-change max change #iterations 11.96266 391.7826 at 10iterations 7.105038 144.9694 at 20iterations 4.199778 80.63025 at 30iterations 2.478245 42.44587 at 40iterations 1.458143 27.56763 at 50iterations 0.8569345 14.90713 at 60iterations 0.5018215 9.103800 at 70iterations 0.2949834 4.555023 at 80iterations 0.1720893 3.106114 at 90iterations 0.1006430 1.782125 at 100iterations 5.8951359E-02 0.8815804 at 110iterations 3.4431919E-02 0.5026627 at 120iterations 2.0118827E-02 0.3209171 at 130iterations 1.1739073E-02 0.1771240 at 140iterations 6.8832240E-03 0.1070557 at 150iterations 4.0309266E-03 6.0923100E-02 at 160iterations 2.3617567E-03 3.6909103E-02 at 170iterations 1.3921296E-03 2.1362305E-02 at 180iterations finished qdiffx linear iterations at : 17:01:26 total time elapsed so far: 13.17000 # loops : 180 mean,max change (kT/e) : 1.3921296E-03 2.1362305E-02 energy calculations done at 13.17000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.31000 DelPhi exited at 17:01:27 13.311u 0.215s 0:14.64 92.3% 0+0k 0+0io 0pf+0w