Sun Oct 9 10:15:11 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 Sun Oct 9 2011 at 10:15:11 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 = 2057 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: 0.6448925 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): -17.85100 31.18100 ymin,ymax (A): 19.17900 74.38200 zmin,zma (A): -2.570000 48.26800 x,y,z range (A): 49.03200 55.20300 50.83800 scale (grids/A): 0.6448925 object centre (A): 6.665000 46.78050 22.84900 number of atom coordinates read : 2057 total number of charged atoms : 1920 net assigned charge : -2.771985 assigned positive charge : 295.7637 centred at (gu) : 89.26806 89.47738 90.69756 assigned negative charge : -298.5364 centred at (gu) : 89.22536 89.75036 90.51981 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 5826 nv = 96 ne = 84 npr = 41803 no. pairs analyzed = 41803 no. exposed pairs = 2763 no. arc points = 18941 no. surface atoms = 929 nbur = 1128 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 319 mr = 3060 m= 3 mr = 55 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 5 time to turn everything in is 0.1600000 number of dielectric boundary points 3033 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1753 ## 128 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 6782 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.0157282E-08 1.5183360E-08 midg,1,midg; midg,igrid,midg 2.5003068E-08 -3.0064157E-08 1,midg,midg; igrid,midg,midg -1.0786103E-08 -4.5513499E-10 gauss-seidel spectral radius is 0.9874987 estimated iterations to convergence 73 setup time was (sec) 0.3700000 now iterating at: 10:15:11 rms-change max change #iterations 0.1312893 26.19633 at 10iterations 1.3140220E-02 2.086059 at 20iterations 1.3217243E-03 0.2219019 at 30iterations 1.3427279E-04 2.3800850E-02 at 40iterations 1.3299629E-05 1.8959045E-03 at 50iterations finished qdiffx linear iterations at : 10:15:14 total time elapsed so far: 3.410000 # loops : 50 mean,max change (kT/e) : 1.3299629E-05 1.8959045E-03 energy calculations done at 3.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.560000 DelPhi exited at 10:15:15 3.562u 0.184s 0:04.16 89.9% 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 Sun Oct 9 2011 at 10:15:15 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 = 2057 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: 1.934677 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): -17.85100 31.18100 ymin,ymax (A): 19.17900 74.38200 zmin,zma (A): -2.570000 48.26800 x,y,z range (A): 49.03200 55.20300 50.83800 scale (grids/A): 1.934677 object centre (A): 6.665000 46.78050 22.84900 number of atom coordinates read : 2057 total number of charged atoms : 1920 net assigned charge : -2.771985 assigned positive charge : 295.7637 centred at (gu) : 87.80395 88.43199 92.09251 assigned negative charge : -298.5364 centred at (gu) : 87.67638 89.25138 91.55955 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 63096 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18941 grid for indexing accessible points = 1.400000 m= 22440 mr = 42773 m= 3617 mr = 16267 m= 244 mr = 2284 m= 3 mr = 112 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 27964 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 91 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 15109 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) : 0.6448925 object centre at (A) : 6.665000 46.78050 22.84900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.2370545E-02 3.0410927E-02 midg,1,midg; midg,igrid,midg 3.1992819E-02 -2.7109805E-02 1,midg,midg; igrid,midg,midg -2.3456443E-02 -1.6179932E-02 gauss-seidel spectral radius is 0.9986252 estimated iterations to convergence 214 setup time was (sec) 0.5400000 now iterating at: 10:15:16 rms-change max change #iterations 3.796092 194.9864 at 10iterations 1.766469 66.97349 at 20iterations 0.8264451 32.40779 at 30iterations 0.3865987 13.72961 at 40iterations 0.1807564 5.950363 at 50iterations 8.4412344E-02 2.787071 at 60iterations 3.9445292E-02 1.296043 at 70iterations 1.8491447E-02 0.6550808 at 80iterations 8.6613586E-03 0.2965088 at 90iterations 4.0276307E-03 0.1360235 at 100iterations 1.8845168E-03 7.2251558E-02 at 110iterations 8.8462274E-04 3.2038212E-02 at 120iterations finished qdiffx linear iterations at : 10:15:23 total time elapsed so far: 7.850000 # loops : 120 mean,max change (kT/e) : 8.8462274E-04 3.2038212E-02 energy calculations done at 7.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.990000 DelPhi exited at 10:15:23 7.991u 0.237s 0:08.51 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 Sun Oct 9 2011 at 10:15:23 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 = 2057 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: 2.902016 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): -17.85100 31.18100 ymin,ymax (A): 19.17900 74.38200 zmin,zma (A): -2.570000 48.26800 x,y,z range (A): 49.03200 55.20300 50.83800 scale (grids/A): 2.902016 object centre (A): 6.665000 46.78050 22.84900 number of atom coordinates read : 2057 total number of charged atoms : 1920 net assigned charge : -2.771985 assigned positive charge : 295.7637 centred at (gu) : 86.70596 87.64780 93.13884 assigned negative charge : -298.5364 centred at (gu) : 86.51466 88.87704 92.33949 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 145788 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18941 grid for indexing accessible points = 1.400000 m= 71891 mr = 103928 m= 26044 mr = 57909 m= 6563 mr = 20743 m= 1074 mr = 5006 m= 85 mr = 776 m= 0 mr = 47 time to grow re-entrant surface = 0.4500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8200000 number of dielectric boundary points 63036 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.9100000 number of grid points assigned charge 15359 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) : 1.934677 object centre at (A) : 6.665000 46.78050 22.84900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5036631 0.3793557 midg,1,midg; midg,igrid,midg 0.2983458 -0.2230824 1,midg,midg; igrid,midg,midg -0.2704287 -0.2052706 gauss-seidel spectral radius is 0.9992506 estimated iterations to convergence 288 setup time was (sec) 1.060000 now iterating at: 10:15:25 rms-change max change #iterations 8.797359 328.2562 at 10iterations 5.101220 114.8389 at 20iterations 2.946635 72.03278 at 30iterations 1.694443 33.54543 at 40iterations 0.9772046 20.06341 at 50iterations 0.5622051 11.86069 at 60iterations 0.3223935 6.422765 at 70iterations 0.1850799 4.053581 at 80iterations 0.1064289 2.333105 at 90iterations 6.1031617E-02 1.260892 at 100iterations 3.4924101E-02 0.7430544 at 110iterations 2.0039931E-02 0.3836546 at 120iterations 1.1484527E-02 0.2280753 at 130iterations 6.5728319E-03 0.1451416 at 140iterations 3.7714206E-03 7.3066711E-02 at 150iterations 2.1535798E-03 3.9903641E-02 at 160iterations 1.2334285E-03 2.5138855E-02 at 170iterations 7.0619321E-04 1.4059067E-02 at 180iterations finished qdiffx linear iterations at : 10:15:36 total time elapsed so far: 12.62000 # loops : 180 mean,max change (kT/e) : 7.0619321E-04 1.4059067E-02 energy calculations done at 12.62000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.76000 DelPhi exited at 10:15:37 12.762u 0.227s 0:13.27 97.8% 0+0k 0+0io 0pf+0w