Wed Dec 28 11:01:14 PST 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 Wed Dec 28 2011 at 11:01:14 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1968 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6162261 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): -35.36400 9.706000 ymin,ymax (A): 1.091000 41.19500 zmin,zma (A): -1.492000 56.27900 x,y,z range (A): 45.07000 40.10400 57.77100 scale (grids/A): 0.6162261 object centre (A): -12.82900 21.14300 27.39350 number of atom coordinates read : 1968 total number of charged atoms : 1836 net assigned charge : 4.000004 assigned positive charge : 287.8741 centred at (gu) : 90.56322 89.65642 90.31757 assigned negative charge : -283.8743 centred at (gu) : 90.51359 89.75313 90.31894 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5056 nv = 96 ne = 84 npr = 40744 no. pairs analyzed = 40744 no. exposed pairs = 2474 no. arc points = 16890 no. surface atoms = 842 nbur = 1126 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 224 mr = 2766 m= 0 mr = 37 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 2477 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1706 ## 180 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 6057 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.7099614E-09 2.9761731E-09 midg,1,midg; midg,igrid,midg 7.5613649E-09 -1.3020132E-09 1,midg,midg; igrid,midg,midg 6.0363253E-10 5.6482210E-09 gauss-seidel spectral radius is 0.9863082 estimated iterations to convergence 70 setup time was (sec) 0.6200000 now iterating at: 11:01:15 rms-change max change #iterations 0.1034216 17.93423 at 10iterations 9.1977036E-03 1.373949 at 20iterations 8.3260104E-04 0.1571331 at 30iterations 7.5384065E-05 1.1577606E-02 at 40iterations 6.7250326E-06 1.1062622E-03 at 50iterations finished qdiffx linear iterations at : 11:01:19 total time elapsed so far: 4.770000 # loops : 50 mean,max change (kT/e) : 6.7250326E-06 1.1062622E-03 energy calculations done at 4.770000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.960000 DelPhi exited at 11:01:21 4.963u 0.412s 0:06.57 81.7% 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 Wed Dec 28 2011 at 11:01:21 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1968 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: 1.848678 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): -35.36400 9.706000 ymin,ymax (A): 1.091000 41.19500 zmin,zma (A): -1.492000 56.27900 x,y,z range (A): 45.07000 40.10400 57.77100 scale (grids/A): 1.848678 object centre (A): -12.82900 21.14300 27.39350 number of atom coordinates read : 1968 total number of charged atoms : 1836 net assigned charge : 4.000004 assigned positive charge : 287.8741 centred at (gu) : 91.68971 88.96928 90.95280 assigned negative charge : -283.8743 centred at (gu) : 91.54098 89.25960 90.95698 start vw surface at 0.1400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 54402 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16890 grid for indexing accessible points = 1.400000 m= 19649 mr = 37573 m= 2799 mr = 14774 m= 134 mr = 1682 m= 0 mr = 51 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5200000 number of dielectric boundary points 22904 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 143 iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 14374 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) : 0.6162261 object centre at (A) : -12.82900 21.14300 27.39350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.0796439E-02 3.0590480E-02 midg,1,midg; midg,igrid,midg 5.4868627E-03 -3.1094248E-03 1,midg,midg; igrid,midg,midg 3.9151058E-04 -1.7601677E-03 gauss-seidel spectral radius is 0.9984755 estimated iterations to convergence 203 setup time was (sec) 0.9100000 now iterating at: 11:01:22 rms-change max change #iterations 3.311143 148.0583 at 10iterations 1.491070 58.17115 at 20iterations 0.6679177 26.85746 at 30iterations 0.2997683 9.982292 at 40iterations 0.1339094 5.008400 at 50iterations 6.0078692E-02 2.152977 at 60iterations 2.7066266E-02 1.039194 at 70iterations 1.2105362E-02 0.4514160 at 80iterations 5.4462533E-03 0.2037773 at 90iterations 2.4397112E-03 8.5306168E-02 at 100iterations 1.0937598E-03 3.8478851E-02 at 110iterations 4.9040862E-04 1.8947601E-02 at 120iterations finished qdiffx linear iterations at : 11:01:33 total time elapsed so far: 11.71000 # loops : 120 mean,max change (kT/e) : 4.9040862E-04 1.8947601E-02 energy calculations done at 11.71000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.90000 DelPhi exited at 11:01:34 11.902u 0.446s 0:13.36 92.3% 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 Wed Dec 28 2011 at 11:01:34 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1968 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: 2.773017 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): -35.36400 9.706000 ymin,ymax (A): 1.091000 41.19500 zmin,zma (A): -1.492000 56.27900 x,y,z range (A): 45.07000 40.10400 57.77100 scale (grids/A): 2.773017 object centre (A): -12.82900 21.14300 27.39350 number of atom coordinates read : 1968 total number of charged atoms : 1836 net assigned charge : 4.000004 assigned positive charge : 287.8741 centred at (gu) : 92.53464 88.45396 91.42913 assigned negative charge : -283.8743 centred at (gu) : 92.31160 88.88945 91.43559 start vw surface at 0.1500000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 125702 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16890 grid for indexing accessible points = 1.400000 m= 64295 mr = 90922 m= 22719 mr = 53101 m= 4786 mr = 18454 m= 566 mr = 3537 m= 22 mr = 396 m= 0 mr = 5 time to grow re-entrant surface = 0.7600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.320000 number of dielectric boundary points 51675 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.510000 number of grid points assigned charge 14684 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) : 1.848678 object centre at (A) : -12.82900 21.14300 27.39350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.5917977E-02 0.2354785 midg,1,midg; midg,igrid,midg 1.9712538E-02 -3.8074374E-02 1,midg,midg; igrid,midg,midg -1.4158454E-02 -6.5637358E-02 gauss-seidel spectral radius is 0.9991950 estimated iterations to convergence 278 setup time was (sec) 1.740000 now iterating at: 11:01:36 rms-change max change #iterations 7.956459 311.6520 at 10iterations 4.563025 140.5800 at 20iterations 2.589321 72.49942 at 30iterations 1.460594 41.84344 at 40iterations 0.8229055 20.17064 at 50iterations 0.4628646 10.64027 at 60iterations 0.2597244 5.559208 at 70iterations 0.1457923 3.008346 at 80iterations 8.1965506E-02 1.727977 at 90iterations 4.5879528E-02 0.9607344 at 100iterations 2.5772784E-02 0.5546012 at 110iterations 1.4399325E-02 0.3077450 at 120iterations 8.0969008E-03 0.1715107 at 130iterations 4.5337449E-03 9.5664978E-02 at 140iterations 2.5357942E-03 5.3081512E-02 at 150iterations 1.4238176E-03 3.0527115E-02 at 160iterations 7.9523574E-04 1.6330719E-02 at 170iterations 4.4534588E-04 8.5859299E-03 at 180iterations finished qdiffx linear iterations at : 11:01:55 total time elapsed so far: 19.66000 # loops : 180 mean,max change (kT/e) : 4.4534588E-04 8.5859299E-03 energy calculations done at 19.66000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.85000 DelPhi exited at 11:01:55 19.847u 0.536s 0:20.96 97.1% 0+0k 0+0io 0pf+0w