Wed Dec 21 14:22:49 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+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 Wed Dec 21 2011 at 14:22:51 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: 265 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6346490 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): -4.318000 36.13700 ymin,ymax (A): -3.676000 49.52500 zmin,zma (A): -24.91100 31.18300 x,y,z range (A): 40.45500 53.20100 56.09400 scale (grids/A): 0.6346490 object centre (A): 15.90950 22.92450 3.136001 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000005 assigned positive charge : 290.6260 centred at (gu) : 90.22581 92.84223 90.36759 assigned negative charge : -288.6263 centred at (gu) : 90.34012 92.98213 90.28588 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 5714 nv = 96 ne = 84 npr = 38331 no. pairs analyzed = 38331 no. exposed pairs = 2637 no. arc points = 18003 no. surface atoms = 897 nbur = 1067 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 380 mr = 3174 m= 2 mr = 76 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 2846 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1866 ## 213 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 6508 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.0300853E-09 9.5485442E-09 midg,1,midg; midg,igrid,midg 7.0949171E-09 -1.4747384E-08 1,midg,midg; igrid,midg,midg 1.0646926E-08 -6.0654113E-09 gauss-seidel spectral radius is 0.9870901 estimated iterations to convergence 72 setup time was (sec) 0.5800000 now iterating at: 14:22:52 rms-change max change #iterations 0.1201610 20.29196 at 10iterations 1.1646798E-02 2.085696 at 20iterations 1.1029757E-03 0.1717720 at 30iterations 1.1032757E-04 1.8754005E-02 at 40iterations 1.0464372E-05 1.7194748E-03 at 50iterations finished qdiffx linear iterations at : 14:22:59 total time elapsed so far: 7.010000 # loops : 50 mean,max change (kT/e) : 1.0464372E-05 1.7194748E-03 energy calculations done at 7.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.210000 DelPhi exited at 14:23:02 7.214u 0.507s 0:10.94 70.4% 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 21 2011 at 14:23:03 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: 265 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.903947 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): -4.318000 36.13700 ymin,ymax (A): -3.676000 49.52500 zmin,zma (A): -24.91100 31.18300 x,y,z range (A): 40.45500 53.20100 56.09400 scale (grids/A): 1.903947 object centre (A): 15.90950 22.92450 3.136001 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000005 assigned positive charge : 290.6260 centred at (gu) : 90.67733 98.52679 91.10266 assigned negative charge : -288.6263 centred at (gu) : 91.02057 98.94646 90.85787 start vw surface at 0.1100000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 60391 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18003 grid for indexing accessible points = 1.400000 m= 25158 mr = 41474 m= 4648 mr = 19653 m= 259 mr = 3256 m= 2 mr = 108 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 167 time to turn everything in is 0.6300000 number of dielectric boundary points 25967 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 130 iepsmp to db, and charging done at 0.8300000 number of grid points assigned charge 14434 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) : 0.6346490 object centre at (A) : 15.90950 22.92450 3.136001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.2329597E-02 1.7520180E-02 midg,1,midg; midg,igrid,midg 3.0556433E-02 -1.5811576E-02 1,midg,midg; igrid,midg,midg 3.7736411E-03 -4.9274070E-03 gauss-seidel spectral radius is 0.9985649 estimated iterations to convergence 209 setup time was (sec) 1.150000 now iterating at: 14:23:05 rms-change max change #iterations 3.581332 201.4072 at 10iterations 1.639589 69.94632 at 20iterations 0.7590213 27.02525 at 30iterations 0.3465455 11.56770 at 40iterations 0.1592551 5.452325 at 50iterations 7.3021740E-02 3.177895 at 60iterations 3.3587448E-02 1.361713 at 70iterations 1.5432044E-02 0.5052910 at 80iterations 7.0899916E-03 0.2384415 at 90iterations 3.2457139E-03 0.1241591 at 100iterations 1.4884322E-03 5.0397396E-02 at 110iterations 6.8636774E-04 2.6365280E-02 at 120iterations finished qdiffx linear iterations at : 14:23:21 total time elapsed so far: 16.98000 # loops : 120 mean,max change (kT/e) : 6.8636774E-04 2.6365280E-02 energy calculations done at 16.98000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.15000 DelPhi exited at 14:23:23 17.156u 0.832s 0:20.56 87.4% 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 21 2011 at 14:23:24 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: 265 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.855920 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): -4.318000 36.13700 ymin,ymax (A): -3.676000 49.52500 zmin,zma (A): -24.91100 31.18300 x,y,z range (A): 40.45500 53.20100 56.09400 scale (grids/A): 2.855920 object centre (A): 15.90950 22.92450 3.136001 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000005 assigned positive charge : 290.6260 centred at (gu) : 91.01611 102.7902 91.65405 assigned negative charge : -288.6263 centred at (gu) : 91.53090 103.4197 91.28691 start vw surface at 0.1200000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 138941 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18003 grid for indexing accessible points = 1.400000 m= 76910 mr = 99761 m= 32704 mr = 64441 m= 8832 mr = 27702 m= 1244 mr = 7193 m= 75 mr = 877 m= 2 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 0.9400000 no. cavity mid-points inaccessible to solvent = 678 time to turn everything in is 1.580000 number of dielectric boundary points 58692 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.810000 number of grid points assigned charge 14656 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) : 1.903947 object centre at (A) : 15.90950 22.92450 3.136001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.8688685 4.2089161E-02 midg,1,midg; midg,igrid,midg 0.3217571 -0.2156947 1,midg,midg; igrid,midg,midg 2.4720969E-02 -2.9088499E-02 gauss-seidel spectral radius is 0.9992287 estimated iterations to convergence 284 setup time was (sec) 2.120000 now iterating at: 14:23:27 rms-change max change #iterations 8.526353 579.7250 at 10iterations 4.915812 138.4717 at 20iterations 2.807059 63.49612 at 30iterations 1.603492 34.23405 at 40iterations 0.9143638 20.17644 at 50iterations 0.5196656 12.63070 at 60iterations 0.2966708 6.576648 at 70iterations 0.1679462 3.332890 at 80iterations 9.5308617E-02 1.802078 at 90iterations 5.4187074E-02 1.131477 at 100iterations 3.0730052E-02 0.6724027 at 110iterations 1.7441031E-02 0.3295505 at 120iterations 9.8962160E-03 0.2221432 at 130iterations 5.6171967E-03 0.1057206 at 140iterations 3.1830955E-03 6.8565369E-02 at 150iterations 1.8043992E-03 3.8551331E-02 at 160iterations 1.0264569E-03 1.9721508E-02 at 170iterations 5.8393320E-04 1.2561798E-02 at 180iterations finished qdiffx linear iterations at : 14:23:54 total time elapsed so far: 29.00000 # loops : 180 mean,max change (kT/e) : 5.8393320E-04 1.2561798E-02 energy calculations done at 29.00000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 29.19000 DelPhi exited at 14:23:55 29.191u 0.849s 0:30.70 97.8% 0+0k 0+0io 0pf+0w