Mon Oct 10 09:13:55 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 09:13:55 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6449276 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): -6.504000 34.37600 ymin,ymax (A): -3.466000 48.13300 zmin,zma (A): -24.22800 30.97200 x,y,z range (A): 40.88000 51.59900 55.20000 scale (grids/A): 0.6449276 object centre (A): 13.93600 22.33350 3.372001 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 291.8259 centred at (gu) : 91.01071 92.47059 90.15261 assigned negative charge : -288.8262 centred at (gu) : 91.12054 92.60025 90.11504 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 5495 nv = 96 ne = 84 npr = 41002 no. pairs analyzed = 41002 no. exposed pairs = 2426 no. arc points = 16898 no. surface atoms = 818 nbur = 1146 mkacc time = 6.0000002E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 294 mr = 3085 m= 1 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 7.0000008E-02 no. cavity mid-points inaccessible to solvent = 9 time to turn everything in is 0.1700000 number of dielectric boundary points 2677 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1672 ## 151 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 6531 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.7179169E-09 9.4503090E-09 midg,1,midg; midg,igrid,midg 1.0733626E-08 -1.3101343E-08 1,midg,midg; igrid,midg,midg 1.3032793E-08 -6.8721566E-09 gauss-seidel spectral radius is 0.9874841 estimated iterations to convergence 73 setup time was (sec) 0.3600000 now iterating at: 09:13:55 rms-change max change #iterations 0.1362360 23.00409 at 10iterations 1.3703660E-02 2.212540 at 20iterations 1.3858324E-03 0.2068729 at 30iterations 1.3797608E-04 2.7046204E-02 at 40iterations 1.3806482E-05 2.5157928E-03 at 50iterations finished qdiffx linear iterations at : 09:13:58 total time elapsed so far: 3.200000 # loops : 50 mean,max change (kT/e) : 1.3806482E-05 2.5157928E-03 energy calculations done at 3.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.330000 DelPhi exited at 09:13:58 3.332u 0.155s 0:03.76 92.5% 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 09:13:58 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.934783 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): -6.504000 34.37600 ymin,ymax (A): -3.466000 48.13300 zmin,zma (A): -24.22800 30.97200 x,y,z range (A): 40.88000 51.59900 55.20000 scale (grids/A): 1.934783 object centre (A): 13.93600 22.33350 3.372001 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 291.8259 centred at (gu) : 93.03221 97.41198 90.45782 assigned negative charge : -288.8262 centred at (gu) : 93.36182 97.80080 90.34525 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 59054 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16898 grid for indexing accessible points = 1.400000 m= 21679 mr = 40969 m= 3537 mr = 16530 m= 207 mr = 2312 m= 3 mr = 84 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 2458 time to turn everything in is 0.3000000 number of dielectric boundary points 24585 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 97 iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 14454 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) : 0.6449276 object centre at (A) : 13.93600 22.33350 3.372001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.0689075E-02 1.6046757E-02 midg,1,midg; midg,igrid,midg 3.6779657E-02 -6.1132275E-03 1,midg,midg; igrid,midg,midg 8.6271111E-03 -7.1772705E-03 gauss-seidel spectral radius is 0.9985952 estimated iterations to convergence 211 setup time was (sec) 0.5200000 now iterating at: 09:13:59 rms-change max change #iterations 3.742488 181.0984 at 10iterations 1.737398 68.64544 at 20iterations 0.8061903 33.01667 at 30iterations 0.3735451 12.93559 at 40iterations 0.1731246 6.410892 at 50iterations 7.9601400E-02 2.969029 at 60iterations 3.7024066E-02 1.309781 at 70iterations 1.7187420E-02 0.5834694 at 80iterations 7.9133902E-03 0.3045101 at 90iterations 3.6731006E-03 0.1272659 at 100iterations 1.6976057E-03 5.5560112E-02 at 110iterations 7.8820315E-04 2.5627136E-02 at 120iterations finished qdiffx linear iterations at : 09:14:06 total time elapsed so far: 7.470000 # loops : 120 mean,max change (kT/e) : 7.8820315E-04 2.5627136E-02 energy calculations done at 7.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.610000 DelPhi exited at 09:14:07 7.609u 0.178s 0:08.37 92.8% 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 Mon Oct 10 2011 at 09:14:07 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.902174 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): -6.504000 34.37600 ymin,ymax (A): -3.466000 48.13300 zmin,zma (A): -24.22800 30.97200 x,y,z range (A): 40.88000 51.59900 55.20000 scale (grids/A): 2.902174 object centre (A): 13.93600 22.33350 3.372001 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 291.8259 centred at (gu) : 94.54826 101.1180 90.68687 assigned negative charge : -288.8262 centred at (gu) : 95.04276 101.7012 90.51797 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 136184 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16898 grid for indexing accessible points = 1.400000 m= 69790 mr = 98627 m= 26235 mr = 58117 m= 6384 mr = 21754 m= 929 mr = 4940 m= 53 mr = 654 m= 0 mr = 20 time to grow re-entrant surface = 0.4200000 no. cavity mid-points inaccessible to solvent = 7861 time to turn everything in is 0.7700000 number of dielectric boundary points 55463 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 14655 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) : 1.934783 object centre at (A) : 13.93600 22.33350 3.372001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.073825 7.2667366E-03 midg,1,midg; midg,igrid,midg 0.3665857 -8.7402269E-02 1,midg,midg; igrid,midg,midg 5.5612683E-02 -5.2471511E-02 gauss-seidel spectral radius is 0.9992341 estimated iterations to convergence 285 setup time was (sec) 1.000000 now iterating at: 09:14:08 rms-change max change #iterations 8.723410 351.0483 at 10iterations 5.014569 112.2807 at 20iterations 2.864359 69.18143 at 30iterations 1.626834 42.05511 at 40iterations 0.9279422 22.33440 at 50iterations 0.5271170 12.73319 at 60iterations 0.2998328 6.563970 at 70iterations 0.1703760 3.574928 at 80iterations 9.6913233E-02 2.034328 at 90iterations 5.4973263E-02 1.320774 at 100iterations 3.1174935E-02 0.6085129 at 110iterations 1.7722981E-02 0.3356838 at 120iterations 1.0064670E-02 0.1866503 at 130iterations 5.7089468E-03 0.1170225 at 140iterations 3.2441914E-03 6.1656952E-02 at 150iterations 1.8413077E-03 3.8810730E-02 at 160iterations 1.0449796E-03 2.1568298E-02 at 170iterations 5.9476861E-04 1.1854172E-02 at 180iterations finished qdiffx linear iterations at : 09:14:19 total time elapsed so far: 11.96000 # loops : 180 mean,max change (kT/e) : 5.9476861E-04 1.1854172E-02 energy calculations done at 11.96000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.08000 DelPhi exited at 09:14:20 12.086u 0.202s 0:12.62 97.3% 0+0k 0+0io 0pf+0w