Tue Oct 11 06:23:53 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 06:23:53 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1330 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.8050474 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): -14.73700 25.58900 ymin,ymax (A): 40.12400 76.44600 zmin,zma (A): -4.722000 39.49900 x,y,z range (A): 40.32600 36.32200 44.22100 scale (grids/A): 0.8050474 object centre (A): 5.426001 58.28500 17.38850 number of atom coordinates read : 1330 total number of charged atoms : 1268 net assigned charge : 2.500002 assigned positive charge : 201.4374 centred at (gu) : 90.05948 90.91207 89.86085 assigned negative charge : -198.9373 centred at (gu) : 90.18312 90.98188 89.57376 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 6466 nv = 96 ne = 84 npr = 24771 no. pairs analyzed = 24771 no. exposed pairs = 1727 no. arc points = 12382 no. surface atoms = 598 nbur = 732 mkacc time = 3.9999999E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 544 mr = 3673 m= 7 mr = 117 m= 0 mr = 0 time to grow re-entrant surface = 4.9999997E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1300000 number of dielectric boundary points 3227 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 884 ## 79 charges are in solution ## iepsmp to db, and charging done at 0.2000000 number of grid points assigned charge 6059 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.7629911E-07 7.4507693E-07 midg,1,midg; midg,igrid,midg 2.6824705E-07 1.5767576E-08 1,midg,midg; igrid,midg,midg 4.2230559E-07 -1.0309996E-07 gauss-seidel spectral radius is 0.9918749 estimated iterations to convergence 90 setup time was (sec) 0.3200000 now iterating at: 06:23:54 rms-change max change #iterations 0.2705954 37.51710 at 10iterations 4.1976858E-02 5.466022 at 20iterations 6.6129933E-03 0.8822241 at 30iterations 1.0502654E-03 0.1449890 at 40iterations 1.8287856E-04 2.4743080E-02 at 50iterations finished qdiffx linear iterations at : 06:23:57 total time elapsed so far: 3.240000 # loops : 50 mean,max change (kT/e) : 1.8287856E-04 2.4743080E-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) 3.370000 DelPhi exited at 06:23:57 3.378u 0.172s 0:04.18 84.6% 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 06:23:57 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1330 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: 2.415142 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): -14.73700 25.58900 ymin,ymax (A): 40.12400 76.44600 zmin,zma (A): -4.722000 39.49900 x,y,z range (A): 40.32600 36.32200 44.22100 scale (grids/A): 2.415142 object centre (A): 5.426001 58.28500 17.38850 number of atom coordinates read : 1330 total number of charged atoms : 1268 net assigned charge : 2.500002 assigned positive charge : 201.4374 centred at (gu) : 90.17889 92.73658 89.58287 assigned negative charge : -198.9373 centred at (gu) : 90.54986 92.94588 88.72153 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 67006 reading accessible surface arcs data from file ARCDAT no. of arc points read = 12382 grid for indexing accessible points = 1.400000 m= 29868 mr = 46806 m= 7758 mr = 23259 m= 1024 mr = 5640 m= 52 mr = 585 m= 0 mr = 11 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 29407 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 15 iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 10129 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) : 0.8050474 object centre at (A) : 5.426001 58.28500 17.38850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.1869280E-02 7.5310335E-02 midg,1,midg; midg,igrid,midg 2.0201748E-02 5.2466965E-03 1,midg,midg; igrid,midg,midg 7.0636764E-02 1.6682334E-02 gauss-seidel spectral radius is 0.9989998 estimated iterations to convergence 250 setup time was (sec) 0.5700000 now iterating at: 06:23:58 rms-change max change #iterations 4.534476 209.0332 at 10iterations 2.374017 78.48136 at 20iterations 1.245282 38.61336 at 30iterations 0.6493465 20.02717 at 40iterations 0.3391869 10.00150 at 50iterations 0.1779086 5.372749 at 60iterations 9.2732042E-02 2.907245 at 70iterations 4.8566073E-02 1.633701 at 80iterations 2.5342645E-02 0.7596612 at 90iterations 1.3342611E-02 0.3843651 at 100iterations 7.0184818E-03 0.2102661 at 110iterations 3.7239520E-03 0.1106772 at 120iterations finished qdiffx linear iterations at : 06:24:05 total time elapsed so far: 7.760000 # loops : 120 mean,max change (kT/e) : 3.7239520E-03 0.1106772 energy calculations done at 7.760000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.890000 DelPhi exited at 06:24:06 7.891u 0.204s 0:08.73 92.6% 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 06:24:06 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1330 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.622713 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): -14.73700 25.58900 ymin,ymax (A): 40.12400 76.44600 zmin,zma (A): -4.722000 39.49900 x,y,z range (A): 40.32600 36.32200 44.22100 scale (grids/A): 3.622713 object centre (A): 5.426001 58.28500 17.38850 number of atom coordinates read : 1330 total number of charged atoms : 1268 net assigned charge : 2.500002 assigned positive charge : 201.4374 centred at (gu) : 90.26846 94.10500 89.37442 assigned negative charge : -198.9373 centred at (gu) : 90.82491 94.41889 88.08229 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 153952 reading accessible surface arcs data from file ARCDAT no. of arc points read = 12382 grid for indexing accessible points = 1.400000 m= 87657 mr = 112223 m= 42063 mr = 73674 m= 15507 mr = 35627 m= 4066 mr = 12594 m= 700 mr = 3092 m= 78 mr = 457 m= 2 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 0.5900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.110000 number of dielectric boundary points 66316 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.200000 number of grid points assigned charge 10144 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) : 2.415142 object centre at (A) : 5.426001 58.28500 17.38850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.6751259 0.4968564 midg,1,midg; midg,igrid,midg 0.1272084 4.7459237E-02 1,midg,midg; igrid,midg,midg 0.4903287 5.4108128E-02 gauss-seidel spectral radius is 0.9993288 estimated iterations to convergence 304 setup time was (sec) 1.350000 now iterating at: 06:24:08 rms-change max change #iterations 9.650723 285.3801 at 10iterations 5.843931 140.4715 at 20iterations 3.510144 85.77452 at 30iterations 2.111103 49.36854 at 40iterations 1.259754 31.93855 at 50iterations 0.7535754 14.16197 at 60iterations 0.4477127 9.189977 at 70iterations 0.2662301 5.114650 at 80iterations 0.1585846 2.842522 at 90iterations 9.4162293E-02 2.058402 at 100iterations 5.5828579E-02 1.020021 at 110iterations 3.3073246E-02 0.5725880 at 120iterations 1.9613190E-02 0.3619127 at 130iterations 1.1639080E-02 0.2135210 at 140iterations 6.8951054E-03 0.1273956 at 150iterations 4.0841438E-03 7.8002930E-02 at 160iterations 2.4339103E-03 4.4326782E-02 at 170iterations 1.4552166E-03 2.9325485E-02 at 180iterations finished qdiffx linear iterations at : 06:24:19 total time elapsed so far: 12.85000 # loops : 180 mean,max change (kT/e) : 1.4552166E-03 2.9325485E-02 energy calculations done at 12.85000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.97000 DelPhi exited at 06:24:20 12.973u 0.236s 0:13.52 97.6% 0+0k 0+0io 0pf+0w