Mon Oct 10 09:45:00 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 09:45:00 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2739 !!! WARNING: HIT 220 has a net charge of 0.5140 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: 0.6011686 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): -16.80100 36.31600 ymin,ymax (A): -64.12800 -4.910000 zmin,zma (A): -3.916000 48.77400 x,y,z range (A): 53.11700 59.21800 52.69000 scale (grids/A): 0.6011686 object centre (A): 9.757499 -34.51900 22.42900 number of atom coordinates read : 2739 total number of charged atoms : 2589 net assigned charge : 2.014010 assigned positive charge : 401.9691 centred at (gu) : 88.84196 89.47437 89.67386 assigned negative charge : -399.9554 centred at (gu) : 88.97570 89.40302 89.62271 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6726 nv = 96 ne = 84 npr = 53690 no. pairs analyzed = 53690 no. exposed pairs = 4200 no. arc points = 30461 no. surface atoms = 1376 nbur = 1363 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 368 mr = 2983 m= 3 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 9.9999987E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 4097 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2920 ## 281 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 8277 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.2411548E-09 2.6343538E-09 midg,1,midg; midg,igrid,midg -2.2041389E-09 3.2059300E-09 1,midg,midg; igrid,midg,midg 7.8172464E-09 -3.3893011E-09 gauss-seidel spectral radius is 0.9857092 estimated iterations to convergence 69 setup time was (sec) 0.4000000 now iterating at: 09:45:00 rms-change max change #iterations 0.1105277 20.34278 at 10iterations 9.3021430E-03 1.663696 at 20iterations 7.7595585E-04 0.1168385 at 30iterations 7.1110000E-05 1.2741089E-02 at 40iterations 8.5773108E-06 1.0929108E-03 at 50iterations finished qdiffx linear iterations at : 09:45:03 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 8.5773108E-06 1.0929108E-03 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.420000 DelPhi exited at 09:45:04 3.419u 0.168s 0:03.87 92.2% 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 09:45:04 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2739 !!! WARNING: HIT 220 has a net charge of 0.5140 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: 1.803506 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): -16.80100 36.31600 ymin,ymax (A): -64.12800 -4.910000 zmin,zma (A): -3.916000 48.77400 x,y,z range (A): 53.11700 59.21800 52.69000 scale (grids/A): 1.803506 object centre (A): 9.757499 -34.51900 22.42900 number of atom coordinates read : 2739 total number of charged atoms : 2589 net assigned charge : 2.014010 assigned positive charge : 401.9691 centred at (gu) : 86.52568 88.42255 89.02139 assigned negative charge : -399.9554 centred at (gu) : 86.92683 88.20877 88.86787 start vw surface at 0.1000000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 71324 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30461 grid for indexing accessible points = 1.400000 m= 23380 mr = 43758 m= 3277 mr = 14702 m= 143 mr = 1494 m= 2 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 97 time to turn everything in is 0.3700000 number of dielectric boundary points 38154 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 234 iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 20230 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) : 0.6011686 object centre at (A) : 9.757499 -34.51900 22.42900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.0021569E-04 -5.0681103E-03 midg,1,midg; midg,igrid,midg 2.0387325E-02 3.6631886E-02 1,midg,midg; igrid,midg,midg 2.0300796E-02 -7.3754904E-03 gauss-seidel spectral radius is 0.9985213 estimated iterations to convergence 206 setup time was (sec) 0.5800000 now iterating at: 09:45:04 rms-change max change #iterations 3.887132 242.1248 at 10iterations 1.756268 68.72432 at 20iterations 0.7958574 26.70166 at 30iterations 0.3602657 13.06014 at 40iterations 0.1632926 5.892829 at 50iterations 7.4109472E-02 2.527105 at 60iterations 3.3537660E-02 1.302143 at 70iterations 1.5245107E-02 0.5198822 at 80iterations 6.9200182E-03 0.2359314 at 90iterations 3.1351161E-03 0.1066017 at 100iterations 1.4228148E-03 4.5242310E-02 at 110iterations 6.4408768E-04 2.5411606E-02 at 120iterations finished qdiffx linear iterations at : 09:45:12 total time elapsed so far: 7.740000 # loops : 120 mean,max change (kT/e) : 6.4408768E-04 2.5411606E-02 energy calculations done at 7.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.880000 DelPhi exited at 09:45:12 7.878u 0.194s 0:08.40 95.9% 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 09:45:12 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2739 !!! WARNING: HIT 220 has a net charge of 0.5140 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: 2.705259 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): -16.80100 36.31600 ymin,ymax (A): -64.12800 -4.910000 zmin,zma (A): -3.916000 48.77400 x,y,z range (A): 53.11700 59.21800 52.69000 scale (grids/A): 2.705259 object centre (A): 9.757499 -34.51900 22.42900 number of atom coordinates read : 2739 total number of charged atoms : 2589 net assigned charge : 2.014010 assigned positive charge : 401.9691 centred at (gu) : 84.78833 87.63389 88.53189 assigned negative charge : -399.9554 centred at (gu) : 85.39014 87.31300 88.30170 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 164637 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30461 grid for indexing accessible points = 1.400000 m= 75168 mr = 107634 m= 25853 mr = 55899 m= 5280 mr = 18487 m= 543 mr = 3131 m= 25 mr = 206 m= 0 mr = 3 time to grow re-entrant surface = 0.5100000 no. cavity mid-points inaccessible to solvent = 408 time to turn everything in is 0.9100000 number of dielectric boundary points 86146 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.000000 number of grid points assigned charge 20711 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) : 1.803506 object centre at (A) : 9.757499 -34.51900 22.42900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.1471074E-02 -5.4687928E-02 midg,1,midg; midg,igrid,midg 0.4271596 0.5271042 1,midg,midg; igrid,midg,midg 0.1994427 -4.0927313E-02 gauss-seidel spectral radius is 0.9992580 estimated iterations to convergence 290 setup time was (sec) 1.140000 now iterating at: 09:45:14 rms-change max change #iterations 9.714714 337.4856 at 10iterations 5.797679 156.8029 at 20iterations 3.415094 81.89729 at 30iterations 2.003897 49.17281 at 40iterations 1.169014 28.54253 at 50iterations 0.6781263 15.24560 at 60iterations 0.3938149 8.685137 at 70iterations 0.2269990 5.556087 at 80iterations 0.1315607 3.134454 at 90iterations 7.6095156E-02 1.835751 at 100iterations 4.3867145E-02 0.9474783 at 110iterations 2.5260171E-02 0.5565929 at 120iterations 1.4545837E-02 0.2949944 at 130iterations 8.3613973E-03 0.1686821 at 140iterations 4.8037316E-03 9.8154068E-02 at 150iterations 2.7561451E-03 5.5383682E-02 at 160iterations 1.5858861E-03 3.5239458E-02 at 170iterations 9.1200322E-04 2.2762299E-02 at 180iterations finished qdiffx linear iterations at : 09:45:25 total time elapsed so far: 12.66000 # loops : 180 mean,max change (kT/e) : 9.1200322E-04 2.2762299E-02 energy calculations done at 12.66000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.79000 DelPhi exited at 09:45:25 12.790u 0.225s 0:13.29 97.8% 0+0k 0+0io 0pf+0w