Tue Oct 11 07:20:15 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+sph.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 = amb.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 Tue Oct 11 2011 at 07:20:15 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: 285 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3275 !!! WARNING: UMP 529 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.5945224 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): 0.1750000 48.96500 ymin,ymax (A): -9.469000 49.07400 zmin,zma (A): 0.8960000 60.77600 x,y,z range (A): 48.79000 58.54300 59.88000 scale (grids/A): 0.5945224 object centre (A): 24.57000 19.80250 30.83600 number of atom coordinates read : 3275 total number of charged atoms : 3103 net assigned charge : -1.599988 assigned positive charge : 488.2478 centred at (gu) : 89.73203 89.84058 90.89424 assigned negative charge : -489.8489 centred at (gu) : 89.65438 89.77229 90.83337 start vw surface at 0.2100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 7575 nv = 96 ne = 84 npr = 68062 no. pairs analyzed = 68062 no. exposed pairs = 3781 no. arc points = 25875 no. surface atoms = 1292 nbur = 1983 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 358 mr = 4423 m= 1 mr = 29 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 20 time to turn everything in is 0.4000000 number of dielectric boundary points 3482 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2611 ## 251 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 9553 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.4084685E-09 2.1846440E-09 midg,1,midg; midg,igrid,midg -3.3720620E-09 1.9730400E-09 1,midg,midg; igrid,midg,midg -3.8513086E-09 2.2587017E-09 gauss-seidel spectral radius is 0.9854090 estimated iterations to convergence 68 setup time was (sec) 0.6200000 now iterating at: 07:20:16 rms-change max change #iterations 0.1155172 16.37806 at 10iterations 1.0279108E-02 1.478951 at 20iterations 1.1698463E-03 0.1775684 at 30iterations 2.2796438E-04 3.6699295E-02 at 40iterations 5.4923370E-05 9.3154907E-03 at 50iterations finished qdiffx linear iterations at : 07:20:18 total time elapsed so far: 3.030000 # loops : 50 mean,max change (kT/e) : 5.4923370E-05 9.3154907E-03 energy calculations done at 3.030000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.200000 DelPhi exited at 07:20:19 3.206u 0.123s 0:03.94 84.2% 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 Tue Oct 11 2011 at 07:20:19 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: 285 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3275 !!! WARNING: UMP 529 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 1.783567 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): 0.1750000 48.96500 ymin,ymax (A): -9.469000 49.07400 zmin,zma (A): 0.8960000 60.77600 x,y,z range (A): 48.79000 58.54300 59.88000 scale (grids/A): 1.783567 object centre (A): 24.57000 19.80250 30.83600 number of atom coordinates read : 3275 total number of charged atoms : 3103 net assigned charge : -1.599988 assigned positive charge : 488.2478 centred at (gu) : 89.19495 89.52093 92.68197 assigned negative charge : -489.8489 centred at (gu) : 88.96269 89.31655 92.49952 start vw surface at 0.2300000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 83740 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25875 grid for indexing accessible points = 1.400000 m= 29771 mr = 60400 m= 3779 mr = 22471 m= 155 mr = 2287 m= 0 mr = 40 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 2244 time to turn everything in is 0.6300000 number of dielectric boundary points 32247 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 230 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 24161 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) : 0.5945224 object centre at (A) : 24.57000 19.80250 30.83600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3075306E-02 7.8554861E-03 midg,1,midg; midg,igrid,midg -1.3988582E-02 4.1725757E-03 1,midg,midg; igrid,midg,midg -1.3139016E-02 2.7130597E-04 gauss-seidel spectral radius is 0.9985098 estimated iterations to convergence 205 setup time was (sec) 0.9100000 now iterating at: 07:20:20 rms-change max change #iterations 4.251873 217.4563 at 10iterations 1.921465 67.41707 at 20iterations 0.8737323 27.40405 at 30iterations 0.3966776 14.37903 at 40iterations 0.1798348 5.264608 at 50iterations 8.1702478E-02 2.608145 at 60iterations 3.7227362E-02 1.131229 at 70iterations 1.6922511E-02 0.5437746 at 80iterations 7.6975082E-03 0.2353363 at 90iterations 3.5184831E-03 0.1045532 at 100iterations 1.6149485E-03 5.0148010E-02 at 110iterations 7.4585463E-04 2.2109985E-02 at 120iterations finished qdiffx linear iterations at : 07:20:26 total time elapsed so far: 6.920000 # loops : 120 mean,max change (kT/e) : 7.4585463E-04 2.2109985E-02 energy calculations done at 6.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.100000 DelPhi exited at 07:20:27 7.099u 0.153s 0:07.56 95.7% 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 Tue Oct 11 2011 at 07:20:27 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: 285 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3275 !!! WARNING: UMP 529 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.675351 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): 0.1750000 48.96500 ymin,ymax (A): -9.469000 49.07400 zmin,zma (A): 0.8960000 60.77600 x,y,z range (A): 48.79000 58.54300 59.88000 scale (grids/A): 2.675351 object centre (A): 24.57000 19.80250 30.83600 number of atom coordinates read : 3275 total number of charged atoms : 3103 net assigned charge : -1.599988 assigned positive charge : 488.2478 centred at (gu) : 88.79234 89.28116 94.02273 assigned negative charge : -489.8489 centred at (gu) : 88.44388 88.97465 93.74918 start vw surface at 0.1700000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 194236 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25875 grid for indexing accessible points = 1.400000 m= 99558 mr = 146230 m= 32751 mr = 83017 m= 6372 mr = 26464 m= 633 mr = 4759 m= 21 mr = 383 m= 0 mr = 12 time to grow re-entrant surface = 0.8200000 no. cavity mid-points inaccessible to solvent = 7524 time to turn everything in is 1.440000 number of dielectric boundary points 72706 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 1.580000 number of grid points assigned charge 24818 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) : 1.783567 object centre at (A) : 24.57000 19.80250 30.83600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3982903 -1.6118612E-02 midg,1,midg; midg,igrid,midg -0.2557119 3.6163509E-02 1,midg,midg; igrid,midg,midg -0.1481593 -2.8822064E-02 gauss-seidel spectral radius is 0.9992319 estimated iterations to convergence 285 setup time was (sec) 1.760000 now iterating at: 07:20:29 rms-change max change #iterations 10.26197 334.4718 at 10iterations 5.908154 117.6563 at 20iterations 3.392310 65.72001 at 30iterations 1.939790 35.89443 at 40iterations 1.107163 22.59007 at 50iterations 0.6328341 11.06285 at 60iterations 0.3603755 6.529648 at 70iterations 0.2057977 3.681131 at 80iterations 0.1169309 2.033207 at 90iterations 6.6672787E-02 1.178719 at 100iterations 3.7971243E-02 0.6870785 at 110iterations 2.1631710E-02 0.4613628 at 120iterations 1.2309119E-02 0.2065239 at 130iterations 7.0254663E-03 0.1213708 at 140iterations 4.0273019E-03 6.7722321E-02 at 150iterations 2.3167080E-03 4.4712067E-02 at 160iterations 1.3422342E-03 2.3143768E-02 at 170iterations 7.8973232E-04 1.4074326E-02 at 180iterations finished qdiffx linear iterations at : 07:20:40 total time elapsed so far: 12.64000 # loops : 180 mean,max change (kT/e) : 7.8973232E-04 1.4074326E-02 energy calculations done at 12.64000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.81000 DelPhi exited at 07:20:40 12.817u 0.260s 0:13.60 96.1% 0+0k 0+0io 0pf+0w