Mon Oct 10 14:15:07 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 14:15:07 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: 325 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3780 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: 0.5561544 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): -1.912000 60.23400 ymin,ymax (A): -18.41200 44.56300 zmin,zma (A): -5.301000 58.71000 x,y,z range (A): 62.14600 62.97500 64.01100 scale (grids/A): 0.5561544 object centre (A): 29.16100 13.07550 26.70450 number of atom coordinates read : 3780 total number of charged atoms : 3629 net assigned charge : -8.999962 assigned positive charge : 576.3663 centred at (gu) : 88.89506 86.76909 90.52347 assigned negative charge : -585.3688 centred at (gu) : 88.97659 86.77389 90.53185 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7643 nv = 96 ne = 84 npr = 76640 no. pairs analyzed = 76640 no. exposed pairs = 4908 no. arc points = 34544 no. surface atoms = 1634 nbur = 2146 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 333 mr = 3948 m= 1 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 4013 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3476 ## 456 charges are in solution ## iepsmp to db, and charging done at 0.3300000 number of grid points assigned charge 10003 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.4194006E-10 -1.0594913E-09 midg,1,midg; midg,igrid,midg -1.6707825E-09 -4.2028039E-10 1,midg,midg; igrid,midg,midg 2.5125607E-10 -1.4265868E-09 gauss-seidel spectral radius is 0.9833882 estimated iterations to convergence 64 setup time was (sec) 0.4500000 now iterating at: 14:15:08 rms-change max change #iterations 9.3329951E-02 14.43959 at 10iterations 6.6257715E-03 1.001186 at 20iterations 5.6131429E-04 9.2704773E-02 at 30iterations 9.0504509E-05 1.7003536E-02 at 40iterations 2.3372355E-05 4.4522285E-03 at 50iterations finished qdiffx linear iterations at : 14:15:11 total time elapsed so far: 3.310000 # loops : 50 mean,max change (kT/e) : 2.3372355E-05 4.4522285E-03 energy calculations done at 3.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.440000 DelPhi exited at 14:15:11 3.448u 0.166s 0:03.99 90.2% 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 Mon Oct 10 2011 at 14:15:11 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: 325 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3780 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: 1.668463 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): -1.912000 60.23400 ymin,ymax (A): -18.41200 44.56300 zmin,zma (A): -5.301000 58.71000 x,y,z range (A): 62.14600 62.97500 64.01100 scale (grids/A): 1.668463 object centre (A): 29.16100 13.07550 26.70450 number of atom coordinates read : 3780 total number of charged atoms : 3629 net assigned charge : -8.999962 assigned positive charge : 576.3663 centred at (gu) : 86.68394 80.30621 91.56931 assigned negative charge : -585.3688 centred at (gu) : 86.92937 80.32121 91.59518 start vw surface at 0.1100000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 84437 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34544 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 26554 mr = 57344 m= 2892 mr = 17973 m= 84 mr = 1364 m= 2 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 29 time to turn everything in is 0.4100000 number of dielectric boundary points 37280 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 389 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 27956 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) : 0.5561544 object centre at (A) : 29.16100 13.07550 26.70450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.6976920E-03 -4.2897873E-03 midg,1,midg; midg,igrid,midg -2.9642640E-02 -8.8748829E-03 1,midg,midg; igrid,midg,midg -1.1238721E-02 -3.6787972E-02 gauss-seidel spectral radius is 0.9983388 estimated iterations to convergence 195 setup time was (sec) 0.6300000 now iterating at: 14:15:12 rms-change max change #iterations 4.054106 175.7201 at 10iterations 1.748068 62.16266 at 20iterations 0.7580124 24.57617 at 30iterations 0.3280266 10.76991 at 40iterations 0.1423040 4.786662 at 50iterations 6.1331112E-02 2.060320 at 60iterations 2.6641754E-02 0.8655453 at 70iterations 1.1541474E-02 0.3955650 at 80iterations 5.0292760E-03 0.1664734 at 90iterations 2.1826928E-03 7.3282242E-02 at 100iterations 9.5216854E-04 3.6159515E-02 at 110iterations 4.2075355E-04 1.3465881E-02 at 120iterations finished qdiffx linear iterations at : 14:15:19 total time elapsed so far: 7.720000 # loops : 120 mean,max change (kT/e) : 4.2075355E-04 1.3465881E-02 energy calculations done at 7.720000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.860000 DelPhi exited at 14:15:20 7.860u 0.189s 0:08.36 96.1% 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 14:15:20 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: 325 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3780 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: 2.502695 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): -1.912000 60.23400 ymin,ymax (A): -18.41200 44.56300 zmin,zma (A): -5.301000 58.71000 x,y,z range (A): 62.14600 62.97500 64.01100 scale (grids/A): 2.502695 object centre (A): 29.16100 13.07550 26.70450 number of atom coordinates read : 3780 total number of charged atoms : 3629 net assigned charge : -8.999962 assigned positive charge : 576.3663 centred at (gu) : 85.02553 75.45910 92.35369 assigned negative charge : -585.3688 centred at (gu) : 85.39381 75.48176 92.39276 start vw surface at 0.1000000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 195685 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34544 grid for indexing accessible points = 1.400000 m= 91537 mr = 140090 m= 26450 mr = 71940 m= 4603 mr = 19574 m= 354 mr = 2902 m= 10 mr = 101 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.5700001 no. cavity mid-points inaccessible to solvent = 95 time to turn everything in is 1.010000 number of dielectric boundary points 84033 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 19 iepsmp to db, and charging done at 1.100000 number of grid points assigned charge 29000 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) : 1.668463 object centre at (A) : 29.16100 13.07550 26.70450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.5368864E-03 0.1222367 midg,1,midg; midg,igrid,midg -0.4282297 -0.1142284 1,midg,midg; igrid,midg,midg -0.1809814 -0.6549289 gauss-seidel spectral radius is 0.9992029 estimated iterations to convergence 280 setup time was (sec) 1.240000 now iterating at: 14:15:21 rms-change max change #iterations 10.41309 292.1641 at 10iterations 5.995662 127.8271 at 20iterations 3.430381 75.52114 at 30iterations 1.953425 37.29591 at 40iterations 1.111361 21.46896 at 50iterations 0.6286314 12.45434 at 60iterations 0.3551444 7.959410 at 70iterations 0.2009591 3.716501 at 80iterations 0.1134465 1.945735 at 90iterations 6.3817225E-02 1.199130 at 100iterations 3.6025546E-02 0.7273483 at 110iterations 2.0286219E-02 0.3846283 at 120iterations 1.1434095E-02 0.2348690 at 130iterations 6.4513902E-03 0.1128192 at 140iterations 3.6332835E-03 6.3860893E-02 at 150iterations 2.0513849E-03 3.8848877E-02 at 160iterations 1.1586382E-03 2.0660400E-02 at 170iterations 6.5704813E-04 1.2351990E-02 at 180iterations finished qdiffx linear iterations at : 14:15:33 total time elapsed so far: 12.77000 # loops : 180 mean,max change (kT/e) : 6.5704813E-04 1.2351990E-02 energy calculations done at 12.77000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.90000 DelPhi exited at 14:15:33 12.899u 0.224s 0:13.59 96.4% 0+0k 0+0io 0pf+0w