Sat Oct 8 12:59:35 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 Sat Oct 8 2011 at 12:59:35 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 = 1303 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: 0.6956929 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): -1.003000 39.60100 ymin,ymax (A): -19.56500 22.96400 zmin,zma (A): -16.99600 34.17600 x,y,z range (A): 40.60400 42.52900 51.17200 scale (grids/A): 0.6956929 object centre (A): 19.29900 1.699499 8.590001 number of atom coordinates read : 1303 total number of charged atoms : 1168 net assigned charge : 3.000018 assigned positive charge : 192.1502 centred at (gu) : 90.27480 88.83362 90.36861 assigned negative charge : -189.1500 centred at (gu) : 90.36100 88.65771 89.79922 start vw surface at 5.9999999E-02 fill in re-entrant regions at 5.9999999E-02 boundary points on vw surface= 4226 nv = 96 ne = 84 npr = 26080 no. pairs analyzed = 26080 no. exposed pairs = 1760 no. arc points = 12682 no. surface atoms = 586 nbur = 717 mkacc time = 5.0000001E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 245 mr = 2106 m= 2 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 5.9999999E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1200000 number of dielectric boundary points 2336 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1030 ## 78 charges are in solution ## iepsmp to db, and charging done at 0.2000000 number of grid points assigned charge 4561 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1016922E-07 1.5387704E-07 midg,1,midg; midg,igrid,midg -2.7608323E-08 4.7028099E-08 1,midg,midg; igrid,midg,midg 3.7110734E-08 -4.4377055E-10 gauss-seidel spectral radius is 0.9891648 estimated iterations to convergence 78 setup time was (sec) 0.3400000 now iterating at: 12:59:35 rms-change max change #iterations 0.1456944 29.66667 at 10iterations 1.6686123E-02 3.336491 at 20iterations 1.9453131E-03 0.2974596 at 30iterations 2.3314699E-04 4.0102005E-02 at 40iterations 2.7677932E-05 4.4116974E-03 at 50iterations finished qdiffx linear iterations at : 12:59:38 total time elapsed so far: 3.550000 # loops : 50 mean,max change (kT/e) : 2.7677932E-05 4.4116974E-03 energy calculations done at 3.550000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.680000 DelPhi exited at 12:59:39 3.687u 0.232s 0:04.22 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 Sat Oct 8 2011 at 12:59:39 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 = 1303 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: 2.087079 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): -1.003000 39.60100 ymin,ymax (A): -19.56500 22.96400 zmin,zma (A): -16.99600 34.17600 x,y,z range (A): 40.60400 42.52900 51.17200 scale (grids/A): 2.087079 object centre (A): 19.29900 1.699499 8.590001 number of atom coordinates read : 1303 total number of charged atoms : 1168 net assigned charge : 3.000018 assigned positive charge : 192.1502 centred at (gu) : 90.82469 86.50107 91.10606 assigned negative charge : -189.1500 centred at (gu) : 91.08303 85.97302 89.39765 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 44266 reading accessible surface arcs data from file ARCDAT no. of arc points read = 12682 grid for indexing accessible points = 1.400000 m= 15573 mr = 28398 m= 2705 mr = 11024 m= 215 mr = 1686 m= 4 mr = 95 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2700000 number of dielectric boundary points 21560 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 34 iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 9253 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) : 0.6956929 object centre at (A) : 19.29900 1.699499 8.590001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.8039770E-02 9.6624918E-02 midg,1,midg; midg,igrid,midg -2.3040576E-02 2.0451196E-02 1,midg,midg; igrid,midg,midg -3.7434645E-04 -3.3885397E-03 gauss-seidel spectral radius is 0.9987208 estimated iterations to convergence 221 setup time was (sec) 0.4900000 now iterating at: 12:59:40 rms-change max change #iterations 3.455565 184.0037 at 10iterations 1.636560 70.14449 at 20iterations 0.7846655 33.90020 at 30iterations 0.3720790 15.55079 at 40iterations 0.1787552 7.715135 at 50iterations 8.5343063E-02 3.244667 at 60iterations 4.0799566E-02 1.579899 at 70iterations 1.9538173E-02 0.7268562 at 80iterations 9.3528638E-03 0.3706226 at 90iterations 4.4760481E-03 0.1950359 at 100iterations 2.1400284E-03 8.7810516E-02 at 110iterations 1.0183358E-03 3.7767410E-02 at 120iterations finished qdiffx linear iterations at : 12:59:47 total time elapsed so far: 8.260000 # loops : 120 mean,max change (kT/e) : 1.0183358E-03 3.7767410E-02 energy calculations done at 8.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.390000 DelPhi exited at 12:59:48 8.389u 0.268s 0:08.98 96.2% 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 12:59:48 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 = 1303 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: 3.130618 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): -1.003000 39.60100 ymin,ymax (A): -19.56500 22.96400 zmin,zma (A): -16.99600 34.17600 x,y,z range (A): 40.60400 42.52900 51.17200 scale (grids/A): 3.130618 object centre (A): 19.29900 1.699499 8.590001 number of atom coordinates read : 1303 total number of charged atoms : 1168 net assigned charge : 3.000018 assigned positive charge : 192.1502 centred at (gu) : 91.23713 84.75154 91.65913 assigned negative charge : -189.1500 centred at (gu) : 91.62453 83.95953 89.09646 start vw surface at 5.9999999E-02 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 102083 reading accessible surface arcs data from file ARCDAT no. of arc points read = 12682 grid for indexing accessible points = 1.400000 m= 48917 mr = 69118 m= 18345 mr = 38843 m= 4872 mr = 14468 m= 943 mr = 3617 m= 114 mr = 678 m= 4 mr = 53 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7200000 number of dielectric boundary points 48501 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 9344 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) : 2.087079 object centre at (A) : 19.29900 1.699499 8.590001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.2566089E-02 0.9888765 midg,1,midg; midg,igrid,midg -0.2419509 0.1952871 1,midg,midg; igrid,midg,midg 1.7926672E-02 -2.0636816E-03 gauss-seidel spectral radius is 0.9992621 estimated iterations to convergence 291 setup time was (sec) 0.9800000 now iterating at: 12:59:49 rms-change max change #iterations 7.800928 401.9755 at 10iterations 4.451962 115.2097 at 20iterations 2.551759 66.63934 at 30iterations 1.462726 35.42105 at 40iterations 0.8384861 20.21187 at 50iterations 0.4807788 10.65985 at 60iterations 0.2749178 5.660821 at 70iterations 0.1573043 3.543612 at 80iterations 9.0282954E-02 2.096024 at 90iterations 5.1561981E-02 1.264069 at 100iterations 2.9578349E-02 0.6163235 at 110iterations 1.6973371E-02 0.3837852 at 120iterations 9.7236466E-03 0.2214645 at 130iterations 5.5611632E-03 0.1256962 at 140iterations 3.1888094E-03 8.0558777E-02 at 150iterations 1.8216553E-03 4.1873932E-02 at 160iterations 1.0488818E-03 2.4193764E-02 at 170iterations 5.9973198E-04 1.3748169E-02 at 180iterations finished qdiffx linear iterations at : 13:00:02 total time elapsed so far: 13.36000 # loops : 180 mean,max change (kT/e) : 5.9973198E-04 1.3748169E-02 energy calculations done at 13.36000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.50000 DelPhi exited at 13:00:02 13.502u 0.279s 0:14.06 97.9% 0+0k 0+0io 0pf+0w