Tue Oct 11 08:20:13 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 Tue Oct 11 2011 at 08:20:14 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: 253 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2120 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6943361 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): -16.07300 28.98500 ymin,ymax (A): -13.04700 35.04100 zmin,zma (A): 1.364000 52.63600 x,y,z range (A): 45.05800 48.08800 51.27200 scale (grids/A): 0.6943361 object centre (A): 6.456000 10.99700 27.00000 number of atom coordinates read : 2120 total number of charged atoms : 2003 net assigned charge : 1.000009 assigned positive charge : 315.4545 centred at (gu) : 90.85670 90.34127 89.54495 assigned negative charge : -314.4549 centred at (gu) : 90.90720 90.32825 89.27598 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7060 nv = 96 ne = 84 npr = 43396 no. pairs analyzed = 43396 no. exposed pairs = 2792 no. arc points = 19612 no. surface atoms = 943 nbur = 1177 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 451 mr = 3843 m= 3 mr = 72 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1800000 number of dielectric boundary points 3599 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1720 ## 139 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 7916 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.0451214E-07 9.4636547E-08 midg,1,midg; midg,igrid,midg 2.0318247E-09 1.2600955E-08 1,midg,midg; igrid,midg,midg 2.1536117E-08 -1.4117878E-08 gauss-seidel spectral radius is 0.9892048 estimated iterations to convergence 78 setup time was (sec) 0.3700000 now iterating at: 08:20:14 rms-change max change #iterations 0.1888760 29.86547 at 10iterations 2.1829586E-02 2.978557 at 20iterations 2.6408266E-03 0.3788376 at 30iterations 3.5954497E-04 5.3478241E-02 at 40iterations 7.1810966E-05 1.2744904E-02 at 50iterations finished qdiffx linear iterations at : 08:20:17 total time elapsed so far: 3.240000 # loops : 50 mean,max change (kT/e) : 7.1810966E-05 1.2744904E-02 energy calculations done at 3.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 08:20:17 3.395u 0.163s 0:03.93 90.3% 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 08:20:17 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: 253 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2120 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.083008 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): -16.07300 28.98500 ymin,ymax (A): -13.04700 35.04100 zmin,zma (A): 1.364000 52.63600 x,y,z range (A): 45.05800 48.08800 51.27200 scale (grids/A): 2.083008 object centre (A): 6.456000 10.99700 27.00000 number of atom coordinates read : 2120 total number of charged atoms : 2003 net assigned charge : 1.000009 assigned positive charge : 315.4545 centred at (gu) : 92.56971 91.02348 88.63471 assigned negative charge : -314.4549 centred at (gu) : 92.72155 90.98469 87.82772 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 75357 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19612 grid for indexing accessible points = 1.400000 m= 27873 mr = 51810 m= 5191 mr = 20398 m= 404 mr = 3309 m= 18 mr = 143 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 21 time to turn everything in is 0.3700000 number of dielectric boundary points 33183 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 98 iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 15875 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) : 0.6943361 object centre at (A) : 6.456000 10.99700 27.00000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.1749985E-02 7.2281696E-02 midg,1,midg; midg,igrid,midg -2.3385637E-02 -3.6120333E-02 1,midg,midg; igrid,midg,midg 1.3626798E-02 -1.4075059E-02 gauss-seidel spectral radius is 0.9988099 estimated iterations to convergence 229 setup time was (sec) 0.5800000 now iterating at: 08:20:18 rms-change max change #iterations 4.536020 227.1140 at 10iterations 2.223154 72.08572 at 20iterations 1.097503 42.42879 at 30iterations 0.5425957 19.32522 at 40iterations 0.2676324 8.713089 at 50iterations 0.1318898 4.340969 at 60iterations 6.4924918E-02 2.135069 at 70iterations 3.2079037E-02 0.9804420 at 80iterations 1.5794232E-02 0.4914856 at 90iterations 7.7908253E-03 0.2412386 at 100iterations 3.8618415E-03 0.1189804 at 110iterations 1.9038579E-03 6.5074921E-02 at 120iterations finished qdiffx linear iterations at : 08:20:25 total time elapsed so far: 7.720000 # loops : 120 mean,max change (kT/e) : 1.9038579E-03 6.5074921E-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) 7.880000 DelPhi exited at 08:20:26 7.883u 0.202s 0:08.37 96.5% 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 Tue Oct 11 2011 at 08:20:26 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: 253 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2120 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.124512 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): -16.07300 28.98500 ymin,ymax (A): -13.04700 35.04100 zmin,zma (A): 1.364000 52.63600 x,y,z range (A): 45.05800 48.08800 51.27200 scale (grids/A): 3.124512 object centre (A): 6.456000 10.99700 27.00000 number of atom coordinates read : 2120 total number of charged atoms : 2003 net assigned charge : 1.000009 assigned positive charge : 315.4545 centred at (gu) : 93.85442 91.53522 87.95187 assigned negative charge : -314.4549 centred at (gu) : 94.08229 91.47694 86.74152 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 174023 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19612 grid for indexing accessible points = 1.400000 m= 87947 mr = 125330 m= 34441 mr = 71620 m= 9536 mr = 27800 m= 1697 mr = 7116 m= 131 mr = 1097 m= 1 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 0.5700000 no. cavity mid-points inaccessible to solvent = 61 time to turn everything in is 1.130000 number of dielectric boundary points 74772 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.220000 number of grid points assigned charge 16016 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) : 2.083008 object centre at (A) : 6.456000 10.99700 27.00000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.7771440 0.6851746 midg,1,midg; midg,igrid,midg -0.2118361 -0.3831048 1,midg,midg; igrid,midg,midg 0.1024584 -0.1397782 gauss-seidel spectral radius is 0.9993067 estimated iterations to convergence 300 setup time was (sec) 1.370000 now iterating at: 08:20:27 rms-change max change #iterations 10.19639 441.8466 at 10iterations 6.004133 130.4311 at 20iterations 3.553485 70.68322 at 30iterations 2.093010 42.98266 at 40iterations 1.231349 21.78317 at 50iterations 0.7215309 13.23295 at 60iterations 0.4240678 8.440677 at 70iterations 0.2492800 4.446918 at 80iterations 0.1456118 2.508331 at 90iterations 8.5357115E-02 1.421967 at 100iterations 4.9971659E-02 0.8518143 at 110iterations 2.9208273E-02 0.5310802 at 120iterations 1.7093608E-02 0.3203888 at 130iterations 1.0015066E-02 0.1769371 at 140iterations 5.8578881E-03 0.1079426 at 150iterations 3.4276841E-03 6.0966492E-02 at 160iterations 2.0060732E-03 3.6570072E-02 at 170iterations 1.1780474E-03 2.0069122E-02 at 180iterations finished qdiffx linear iterations at : 08:20:39 total time elapsed so far: 12.81000 # loops : 180 mean,max change (kT/e) : 1.1780474E-03 2.0069122E-02 energy calculations done at 12.81000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.94000 DelPhi exited at 08:20:40 12.941u 0.207s 0:14.15 92.8% 0+0k 0+0io 0pf+0w