Tue Oct 11 06:28:54 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 Tue Oct 11 2011 at 06:28:54 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2132 !!! WARNING: HIQ 57 has a net charge of 0.5140 !!! WARNING: SEP 195 has a net charge of -0.4750 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: 0.6990948 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): 2.687000 43.41300 ymin,ymax (A): 6.847000 51.04400 zmin,zma (A): 2.151000 53.07400 x,y,z range (A): 40.72600 44.19700 50.92300 scale (grids/A): 0.6990948 object centre (A): 23.05000 28.94550 27.61250 number of atom coordinates read : 2132 total number of charged atoms : 2002 net assigned charge : 6.039011 assigned positive charge : 328.6419 centred at (gu) : 89.19743 89.86734 88.88670 assigned negative charge : -322.6031 centred at (gu) : 89.09276 89.94669 88.84255 start vw surface at 0.1400000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6820 nv = 96 ne = 84 npr = 42583 no. pairs analyzed = 42583 no. exposed pairs = 2911 no. arc points = 19209 no. surface atoms = 979 nbur = 1153 mkacc time = 8.9999989E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 509 mr = 3614 m= 5 mr = 68 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 0.2600000 number of dielectric boundary points 3652 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1758 ## 168 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 7712 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.8827809E-08 4.9134648E-08 midg,1,midg; midg,igrid,midg 7.7552109E-08 8.3191214E-09 1,midg,midg; igrid,midg,midg -3.3305900E-09 7.3600873E-08 gauss-seidel spectral radius is 0.9893392 estimated iterations to convergence 79 setup time was (sec) 0.5000000 now iterating at: 06:28:55 rms-change max change #iterations 0.1975715 28.90367 at 10iterations 2.3925912E-02 3.832079 at 20iterations 3.1953568E-03 0.5207729 at 30iterations 7.5449032E-04 9.3101501E-02 at 40iterations 2.7663083E-04 3.2558441E-02 at 50iterations finished qdiffx linear iterations at : 06:28:57 total time elapsed so far: 3.090000 # loops : 50 mean,max change (kT/e) : 2.7663083E-04 3.2558441E-02 energy calculations done at 3.090000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.260000 DelPhi exited at 06:28:58 3.260u 0.174s 0:03.81 90.0% 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 06:28:58 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2132 !!! WARNING: HIQ 57 has a net charge of 0.5140 !!! WARNING: SEP 195 has a net charge of -0.4750 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: 2.097284 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): 2.687000 43.41300 ymin,ymax (A): 6.847000 51.04400 zmin,zma (A): 2.151000 53.07400 x,y,z range (A): 40.72600 44.19700 50.92300 scale (grids/A): 2.097284 object centre (A): 23.05000 28.94550 27.61250 number of atom coordinates read : 2132 total number of charged atoms : 2002 net assigned charge : 6.039011 assigned positive charge : 328.6419 centred at (gu) : 87.59219 89.60197 86.65997 assigned negative charge : -322.6031 centred at (gu) : 87.27850 89.84010 86.52766 start vw surface at 0.1500000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 70735 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19209 grid for indexing accessible points = 1.400000 m= 28664 mr = 47883 m= 5945 mr = 20619 m= 585 mr = 3627 m= 16 mr = 232 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5500000 number of dielectric boundary points 33584 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 80 iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 15890 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) : 0.6990948 object centre at (A) : 23.05000 28.94550 27.61250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.1710597E-02 1.1228098E-02 midg,1,midg; midg,igrid,midg 2.6324430E-02 1.5358214E-02 1,midg,midg; igrid,midg,midg 9.3722058E-04 3.9946049E-02 gauss-seidel spectral radius is 0.9988138 estimated iterations to convergence 230 setup time was (sec) 0.8100000 now iterating at: 06:28:59 rms-change max change #iterations 4.620575 182.2025 at 10iterations 2.278457 74.58938 at 20iterations 1.118066 35.57364 at 30iterations 0.5516678 17.59488 at 40iterations 0.2726272 8.034046 at 50iterations 0.1346812 3.949274 at 60iterations 6.6422142E-02 2.038727 at 70iterations 3.2849312E-02 1.108065 at 80iterations 1.6416445E-02 0.4816742 at 90iterations 8.2372716E-03 0.2581410 at 100iterations 4.2504431E-03 0.1464386 at 110iterations 2.2784891E-03 7.8132629E-02 at 120iterations finished qdiffx linear iterations at : 06:29:05 total time elapsed so far: 6.810000 # loops : 120 mean,max change (kT/e) : 2.2784891E-03 7.8132629E-02 energy calculations done at 6.810000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.980000 DelPhi exited at 06:29:05 6.984u 0.158s 0:07.69 92.7% 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 06:29:05 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2132 !!! WARNING: HIQ 57 has a net charge of 0.5140 !!! WARNING: SEP 195 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 3.145926 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): 2.687000 43.41300 ymin,ymax (A): 6.847000 51.04400 zmin,zma (A): 2.151000 53.07400 x,y,z range (A): 40.72600 44.19700 50.92300 scale (grids/A): 3.145926 object centre (A): 23.05000 28.94550 27.61250 number of atom coordinates read : 2132 total number of charged atoms : 2002 net assigned charge : 6.039011 assigned positive charge : 328.6419 centred at (gu) : 86.38824 89.40291 84.98994 assigned negative charge : -322.6031 centred at (gu) : 85.91776 89.76018 84.79152 start vw surface at 0.1900000 fill in re-entrant regions at 0.8000000 boundary points on vw surface= 162916 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19209 grid for indexing accessible points = 1.400000 m= 87484 mr = 116392 m= 36879 mr = 70014 m= 11254 mr = 29223 m= 2274 mr = 8110 m= 303 mr = 1438 m= 11 mr = 162 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.8300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.730000 number of dielectric boundary points 75778 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.850000 number of grid points assigned charge 16016 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) : 2.097284 object centre at (A) : 23.05000 28.94550 27.61250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4056643 -6.4228550E-02 midg,1,midg; midg,igrid,midg 0.1828411 0.1993518 1,midg,midg; igrid,midg,midg -3.1756511E-04 0.4079023 gauss-seidel spectral radius is 0.9993042 estimated iterations to convergence 299 setup time was (sec) 2.010000 now iterating at: 06:29:08 rms-change max change #iterations 10.55434 340.5752 at 10iterations 6.365549 154.1296 at 20iterations 3.817778 88.58829 at 30iterations 2.271701 47.55496 at 40iterations 1.354341 26.37999 at 50iterations 0.8015568 17.00266 at 60iterations 0.4754274 8.386765 at 70iterations 0.2805476 5.398609 at 80iterations 0.1653928 2.867374 at 90iterations 9.7509131E-02 1.658051 at 100iterations 5.7447992E-02 1.112085 at 110iterations 3.3855300E-02 0.6480598 at 120iterations 2.0043699E-02 0.3633575 at 130iterations 1.1934129E-02 0.2484493 at 140iterations 7.1932930E-03 0.1299596 at 150iterations 4.4694887E-03 8.5309982E-02 at 160iterations 2.9013087E-03 5.4994583E-02 at 170iterations 2.0076572E-03 3.3432007E-02 at 180iterations finished qdiffx linear iterations at : 06:29:17 total time elapsed so far: 11.42000 # loops : 180 mean,max change (kT/e) : 2.0076572E-03 3.3432007E-02 energy calculations done at 11.42000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.60000 DelPhi exited at 06:29:18 11.601u 0.188s 0:12.44 94.6% 0+0k 0+0io 0pf+0w