Sun Oct 9 10:34:17 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 Sun Oct 9 2011 at 10:34:17 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2959 !!! WARNING: CME 113 has a net charge of -0.3480 !!! WARNING: HIR 211 has a net charge of 0.5140 !!! WARNING: CME 217 has a net charge of -0.3480 !!! WARNING: CME 312 has a net charge of -0.3480 !!! WARNING: CME 456 has a net charge of -0.3480 !!! WARNING: CME 1 has a net charge of -0.0350 !!! WARNING: CME 3 has a net charge of -0.0350 !!! WARNING: CME 5 has a net charge of -0.0350 !!! WARNING: CME 7 has a net charge of -0.0350 !!! WARNING: CME 9 has a net charge of -0.0350 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: 0.5822512 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): -22.05900 39.08300 ymin,ymax (A): -25.34600 24.20900 zmin,zma (A): -28.78300 26.57400 x,y,z range (A): 61.14200 49.55500 55.35700 scale (grids/A): 0.5822512 object centre (A): 8.512000 -0.5684996 -1.104500 number of atom coordinates read : 2959 total number of charged atoms : 2834 net assigned charge : 0.4470298 assigned positive charge : 436.5489 centred at (gu) : 89.72640 91.16742 91.31056 assigned negative charge : -436.1037 centred at (gu) : 89.66030 91.08948 91.26356 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6849 nv = 96 ne = 84 npr = 58534 no. pairs analyzed = 58534 no. exposed pairs = 4002 no. arc points = 27816 no. surface atoms = 1324 nbur = 1635 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 = 1.484000 m= 360 mr = 3488 m= 3 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 3699 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2789 ## 282 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 8667 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.5140705E-10 1.5797834E-09 midg,1,midg; midg,igrid,midg -1.3301171E-09 2.4612212E-09 1,midg,midg; igrid,midg,midg -1.5737190E-09 1.4931396E-09 gauss-seidel spectral radius is 0.9847848 estimated iterations to convergence 67 setup time was (sec) 0.5200000 now iterating at: 10:34:18 rms-change max change #iterations 9.9725388E-02 18.67425 at 10iterations 8.2001034E-03 1.209238 at 20iterations 9.6689106E-04 0.1588249 at 30iterations 2.2970853E-04 3.8801193E-02 at 40iterations 6.9150854E-05 1.1753082E-02 at 50iterations finished qdiffx linear iterations at : 10:34:20 total time elapsed so far: 3.010000 # loops : 50 mean,max change (kT/e) : 6.9150854E-05 1.1753082E-02 energy calculations done at 3.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.190000 DelPhi exited at 10:34:21 3.190u 0.195s 0:03.68 91.8% 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 Sun Oct 9 2011 at 10:34:21 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2959 !!! WARNING: CME 113 has a net charge of -0.3480 !!! WARNING: HIR 211 has a net charge of 0.5140 !!! WARNING: CME 217 has a net charge of -0.3480 !!! WARNING: CME 312 has a net charge of -0.3480 !!! WARNING: CME 456 has a net charge of -0.3480 !!! WARNING: CME 1 has a net charge of -0.0350 !!! WARNING: CME 3 has a net charge of -0.0350 !!! WARNING: CME 5 has a net charge of -0.0350 !!! WARNING: CME 7 has a net charge of -0.0350 !!! WARNING: CME 9 has a net charge of -0.0350 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: 1.746753 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): -22.05900 39.08300 ymin,ymax (A): -25.34600 24.20900 zmin,zma (A): -28.78300 26.57400 x,y,z range (A): 61.14200 49.55500 55.35700 scale (grids/A): 1.746753 object centre (A): 8.512000 -0.5684996 -1.104500 number of atom coordinates read : 2959 total number of charged atoms : 2834 net assigned charge : 0.4470298 assigned positive charge : 436.5489 centred at (gu) : 89.17843 93.50108 93.93052 assigned negative charge : -436.1037 centred at (gu) : 88.98079 93.26806 93.79040 start vw surface at 0.1600000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 75617 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27816 grid for indexing accessible points = 1.400000 m= 24916 mr = 51367 m= 3389 mr = 16837 m= 158 mr = 1690 m= 1 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 245 time to turn everything in is 0.5300000 number of dielectric boundary points 34157 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 203 iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 22065 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) : 0.5822512 object centre at (A) : 8.512000 -0.5684996 -1.104500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.7725815E-03 8.0861403E-03 midg,1,midg; midg,igrid,midg -4.5777281E-04 2.0927105E-02 1,midg,midg; igrid,midg,midg -1.3541997E-03 -4.1263774E-03 gauss-seidel spectral radius is 0.9984381 estimated iterations to convergence 201 setup time was (sec) 0.8000000 now iterating at: 10:34:22 rms-change max change #iterations 3.818260 177.8776 at 10iterations 1.688861 60.44510 at 20iterations 0.7503380 25.62292 at 30iterations 0.3333448 10.55576 at 40iterations 0.1483631 4.941689 at 50iterations 6.5696225E-02 2.346081 at 60iterations 2.9237894E-02 0.9296203 at 70iterations 1.3117194E-02 0.4574738 at 80iterations 5.8957944E-03 0.1942787 at 90iterations 2.6909045E-03 9.2544556E-02 at 100iterations 1.2641302E-03 4.4631958E-02 at 110iterations 6.2155200E-04 2.1746159E-02 at 120iterations finished qdiffx linear iterations at : 10:34:28 total time elapsed so far: 7.150000 # loops : 120 mean,max change (kT/e) : 6.2155200E-04 2.1746159E-02 energy calculations done at 7.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.330000 DelPhi exited at 10:34:28 7.332u 0.212s 0:07.84 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 Sun Oct 9 2011 at 10:34:28 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2959 !!! WARNING: CME 113 has a net charge of -0.3480 !!! WARNING: HIR 211 has a net charge of 0.5140 !!! WARNING: CME 217 has a net charge of -0.3480 !!! WARNING: CME 312 has a net charge of -0.3480 !!! WARNING: CME 456 has a net charge of -0.3480 !!! WARNING: CME 1 has a net charge of -0.0350 !!! WARNING: CME 3 has a net charge of -0.0350 !!! WARNING: CME 5 has a net charge of -0.0350 !!! WARNING: CME 7 has a net charge of -0.0350 !!! WARNING: CME 9 has a net charge of -0.0350 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: 2.620130 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): -22.05900 39.08300 ymin,ymax (A): -25.34600 24.20900 zmin,zma (A): -28.78300 26.57400 x,y,z range (A): 61.14200 49.55500 55.35700 scale (grids/A): 2.620130 object centre (A): 8.512000 -0.5684996 -1.104500 number of atom coordinates read : 2959 total number of charged atoms : 2834 net assigned charge : 0.4470298 assigned positive charge : 436.5489 centred at (gu) : 88.76753 95.25140 95.89578 assigned negative charge : -436.1037 centred at (gu) : 88.47109 94.90211 95.68566 start vw surface at 0.1500000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 175479 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27816 grid for indexing accessible points = 1.400000 m= 83019 mr = 125946 m= 26775 mr = 64864 m= 5515 mr = 19795 m= 589 mr = 3449 m= 18 mr = 306 m= 0 mr = 2 time to grow re-entrant surface = 0.7500000 no. cavity mid-points inaccessible to solvent = 733 time to turn everything in is 1.280000 number of dielectric boundary points 77033 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 1.430000 number of grid points assigned charge 22665 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) : 1.746753 object centre at (A) : 8.512000 -0.5684996 -1.104500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.4448934E-02 0.1084129 midg,1,midg; midg,igrid,midg 5.8240462E-02 0.2881224 1,midg,midg; igrid,midg,midg 8.6023889E-02 -9.1697335E-02 gauss-seidel spectral radius is 0.9992170 estimated iterations to convergence 282 setup time was (sec) 1.590000 now iterating at: 10:34:30 rms-change max change #iterations 9.493304 257.8043 at 10iterations 5.526278 142.9034 at 20iterations 3.190956 77.17300 at 30iterations 1.831922 42.28001 at 40iterations 1.049858 25.11398 at 50iterations 0.5987269 13.21320 at 60iterations 0.3414118 7.000251 at 70iterations 0.1942485 3.747282 at 80iterations 0.1103858 2.364773 at 90iterations 6.2716715E-02 1.191597 at 100iterations 3.5538189E-02 0.7243671 at 110iterations 2.0198202E-02 0.3995209 at 120iterations 1.1471570E-02 0.2136021 at 130iterations 6.5207696E-03 0.1275373 at 140iterations 3.7188451E-03 6.9950104E-02 at 150iterations 2.1380181E-03 4.0542603E-02 at 160iterations 1.2403437E-03 2.6884079E-02 at 170iterations 7.3528144E-04 1.4998436E-02 at 180iterations finished qdiffx linear iterations at : 10:34:40 total time elapsed so far: 11.72000 # loops : 180 mean,max change (kT/e) : 7.3528144E-04 1.4998436E-02 energy calculations done at 11.72000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.89000 DelPhi exited at 10:34:41 11.893u 0.214s 0:12.38 97.7% 0+0k 0+0io 0pf+0w