Sat Oct 8 11:38:38 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 Sat Oct 8 2011 at 11:38:38 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: 285 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2855 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6282538 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): -4.709000 51.95600 ymin,ymax (A): 34.25200 82.35700 zmin,zma (A): 29.81200 85.08400 x,y,z range (A): 56.66500 48.10500 55.27200 scale (grids/A): 0.6282538 object centre (A): 23.62350 58.30450 57.44800 number of atom coordinates read : 2855 total number of charged atoms : 2704 net assigned charge : 8.9108944E-06 assigned positive charge : 421.7503 centred at (gu) : 90.03220 89.51401 88.26089 assigned negative charge : -421.7511 centred at (gu) : 89.98474 89.52197 88.22221 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7763 nv = 96 ne = 84 npr = 55723 no. pairs analyzed = 55723 no. exposed pairs = 3949 no. arc points = 28021 no. surface atoms = 1321 nbur = 1534 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 409 mr = 3900 m= 5 mr = 44 m= 0 mr = 0 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 4233 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2781 ## 238 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 9292 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.1383515E-09 2.4412783E-09 midg,1,midg; midg,igrid,midg 8.7969421E-10 -5.9413635E-10 1,midg,midg; igrid,midg,midg -4.2558659E-09 4.4011723E-09 gauss-seidel spectral radius is 0.9869123 estimated iterations to convergence 72 setup time was (sec) 0.6400000 now iterating at: 11:38:39 rms-change max change #iterations 0.1367844 21.01557 at 10iterations 1.2857080E-02 1.801398 at 20iterations 1.2322405E-03 0.1699190 at 30iterations 1.1653789E-04 1.9852281E-02 at 40iterations 1.1164836E-05 1.4495850E-03 at 50iterations finished qdiffx linear iterations at : 11:38:42 total time elapsed so far: 3.970000 # loops : 50 mean,max change (kT/e) : 1.1164836E-05 1.4495850E-03 energy calculations done at 3.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.150000 DelPhi exited at 11:38:42 4.149u 0.274s 0:04.77 92.4% 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 Sat Oct 8 2011 at 11:38:42 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: 285 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2855 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.884761 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): -4.709000 51.95600 ymin,ymax (A): 34.25200 82.35700 zmin,zma (A): 29.81200 85.08400 x,y,z range (A): 56.66500 48.10500 55.27200 scale (grids/A): 1.884761 object centre (A): 23.62350 58.30450 57.44800 number of atom coordinates read : 2855 total number of charged atoms : 2704 net assigned charge : 8.9108944E-06 assigned positive charge : 421.7503 centred at (gu) : 90.09577 88.54127 84.78189 assigned negative charge : -421.7511 centred at (gu) : 89.95377 88.56551 84.66641 start vw surface at 0.1600000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 83050 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28021 grid for indexing accessible points = 1.400000 m= 28722 mr = 54929 m= 4470 mr = 19993 m= 297 mr = 2549 m= 3 mr = 125 m= 0 mr = 0 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7300000 number of dielectric boundary points 38946 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 212 iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 21269 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) : 0.6282538 object centre at (A) : 23.62350 58.30450 57.44800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.0172764E-02 1.1722877E-02 midg,1,midg; midg,igrid,midg 1.7966526E-02 5.4404363E-03 1,midg,midg; igrid,midg,midg -1.3006164E-02 -1.2328999E-02 gauss-seidel spectral radius is 0.9986498 estimated iterations to convergence 216 setup time was (sec) 1.040000 now iterating at: 11:38:44 rms-change max change #iterations 4.335245 190.4233 at 10iterations 2.036986 67.08136 at 20iterations 0.9603630 29.83047 at 30iterations 0.4490935 13.73088 at 40iterations 0.2115657 6.765014 at 50iterations 9.8915055E-02 3.056525 at 60iterations 4.6347704E-02 1.453968 at 70iterations 2.1782959E-02 0.6732907 at 80iterations 1.0234781E-02 0.3228636 at 90iterations 4.8022834E-03 0.1506186 at 100iterations 2.2591131E-03 7.0058823E-02 at 110iterations 1.0641593E-03 3.5243034E-02 at 120iterations finished qdiffx linear iterations at : 11:38:52 total time elapsed so far: 9.510000 # loops : 120 mean,max change (kT/e) : 1.0641593E-03 3.5243034E-02 energy calculations done at 9.510000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.680000 DelPhi exited at 11:38:53 9.684u 0.305s 0:10.45 95.5% 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 Sat Oct 8 2011 at 11:38:53 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: 285 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2855 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.827142 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): -4.709000 51.95600 ymin,ymax (A): 34.25200 82.35700 zmin,zma (A): 29.81200 85.08400 x,y,z range (A): 56.66500 48.10500 55.27200 scale (grids/A): 2.827142 object centre (A): 23.62350 58.30450 57.44800 number of atom coordinates read : 2855 total number of charged atoms : 2704 net assigned charge : 8.9108944E-06 assigned positive charge : 421.7503 centred at (gu) : 90.14354 87.81176 82.17257 assigned negative charge : -421.7511 centred at (gu) : 89.93047 87.84827 81.99946 start vw surface at 0.1600000 fill in re-entrant regions at 0.6200000 boundary points on vw surface= 192263 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28021 grid for indexing accessible points = 1.400000 m= 93191 mr = 134225 m= 32444 mr = 73606 m= 7790 mr = 24916 m= 1225 mr = 5612 m= 100 mr = 814 m= 1 mr = 50 m= 0 mr = 0 time to grow re-entrant surface = 1.160000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.910000 number of dielectric boundary points 87791 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.070000 number of grid points assigned charge 21631 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) : 1.884761 object centre at (A) : 23.62350 58.30450 57.44800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.5125297E-02 5.7591509E-02 midg,1,midg; midg,igrid,midg 0.2249231 6.4051732E-02 1,midg,midg; igrid,midg,midg 6.8684340E-02 -0.1782204 gauss-seidel spectral radius is 0.9992825 estimated iterations to convergence 295 setup time was (sec) 2.250000 now iterating at: 11:38:56 rms-change max change #iterations 10.50409 328.0008 at 10iterations 6.308316 134.0152 at 20iterations 3.740980 74.09417 at 30iterations 2.208452 43.73061 at 40iterations 1.297937 24.99323 at 50iterations 0.7615937 13.56062 at 60iterations 0.4447837 8.458862 at 70iterations 0.2601459 5.062744 at 80iterations 0.1512557 2.667236 at 90iterations 8.8023193E-02 1.594544 at 100iterations 5.1228918E-02 0.8933525 at 110iterations 2.9708065E-02 0.6118608 at 120iterations 1.7294586E-02 0.2824001 at 130iterations 1.0044700E-02 0.1741896 at 140iterations 5.8273403E-03 9.9427223E-02 at 150iterations 3.3789156E-03 5.6625366E-02 at 160iterations 1.9614859E-03 3.3973694E-02 at 170iterations 1.1369392E-03 2.1152496E-02 at 180iterations finished qdiffx linear iterations at : 11:39:10 total time elapsed so far: 16.47000 # loops : 180 mean,max change (kT/e) : 1.1369392E-03 2.1152496E-02 energy calculations done at 16.47000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.65000 DelPhi exited at 11:39:11 16.647u 0.299s 0:17.53 96.5% 0+0k 0+0io 0pf+0w