Tue Oct 11 06:20:55 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 06:20:55 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: 316 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2034 !!! WARNING: SEP 190 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6849710 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): 17.22400 63.72700 ymin,ymax (A): -3.557000 34.05600 zmin,zma (A): 18.83700 70.81000 x,y,z range (A): 46.50300 37.61300 51.97300 scale (grids/A): 0.6849710 object centre (A): 40.47550 15.24950 44.82350 number of atom coordinates read : 2034 total number of charged atoms : 1950 net assigned charge : 6.025006 assigned positive charge : 318.1521 centred at (gu) : 90.67490 89.48809 89.95535 assigned negative charge : -312.1271 centred at (gu) : 90.82623 89.54646 89.96674 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6531 nv = 96 ne = 84 npr = 39334 no. pairs analyzed = 39334 no. exposed pairs = 2545 no. arc points = 17757 no. surface atoms = 862 nbur = 1172 mkacc time = 5.9999995E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 413 mr = 3609 m= 1 mr = 58 m= 0 mr = 0 time to grow re-entrant surface = 7.0000000E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1800000 number of dielectric boundary points 3278 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1810 ## 198 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 7547 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.3294622E-08 2.6072977E-08 midg,1,midg; midg,igrid,midg 5.1758946E-08 1.1282319E-08 1,midg,midg; igrid,midg,midg 6.4280783E-08 -1.8256763E-08 gauss-seidel spectral radius is 0.9888952 estimated iterations to convergence 77 setup time was (sec) 0.3700000 now iterating at: 06:20:56 rms-change max change #iterations 0.1766534 27.55993 at 10iterations 2.0159392E-02 2.968914 at 20iterations 2.3680709E-03 0.3218117 at 30iterations 3.2233476E-04 4.7447205E-02 at 40iterations 5.7811390E-05 9.5977783E-03 at 50iterations finished qdiffx linear iterations at : 06:20:59 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 5.7811390E-05 9.5977783E-03 energy calculations done at 3.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 06:20:59 3.388u 0.163s 0:04.14 85.5% 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 Tue Oct 11 2011 at 06:20:59 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: 316 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2034 !!! WARNING: SEP 190 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.054913 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): 17.22400 63.72700 ymin,ymax (A): -3.557000 34.05600 zmin,zma (A): 18.83700 70.81000 x,y,z range (A): 46.50300 37.61300 51.97300 scale (grids/A): 2.054913 object centre (A): 40.47550 15.24950 44.82350 number of atom coordinates read : 2034 total number of charged atoms : 1950 net assigned charge : 6.025006 assigned positive charge : 318.1521 centred at (gu) : 92.02467 88.46436 89.86639 assigned negative charge : -312.1271 centred at (gu) : 92.47888 88.63936 89.90023 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 69647 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17757 grid for indexing accessible points = 1.400000 m= 27191 mr = 48646 m= 4928 mr = 20250 m= 415 mr = 3214 m= 13 mr = 197 m= 0 mr = 5 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 29882 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 113 iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 15465 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) : 0.6849710 object centre at (A) : 40.47550 15.24950 44.82350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.4033002E-02 4.6866078E-02 midg,1,midg; midg,igrid,midg 2.7539175E-02 -5.7424344E-03 1,midg,midg; igrid,midg,midg 2.8849313E-02 1.2438019E-02 gauss-seidel spectral radius is 0.9987626 estimated iterations to convergence 225 setup time was (sec) 0.5600000 now iterating at: 06:21:00 rms-change max change #iterations 4.379982 271.0641 at 10iterations 2.133213 84.95376 at 20iterations 1.032282 32.96559 at 30iterations 0.5036733 15.66816 at 40iterations 0.2445466 7.385588 at 50iterations 0.1188287 4.004812 at 60iterations 5.7890844E-02 1.812256 at 70iterations 2.8160939E-02 0.8966169 at 80iterations 1.3705114E-02 0.4037166 at 90iterations 6.6645504E-03 0.2059441 at 100iterations 3.2675380E-03 0.1121626 at 110iterations 1.6016281E-03 5.2015305E-02 at 120iterations finished qdiffx linear iterations at : 06:21:07 total time elapsed so far: 7.640000 # loops : 120 mean,max change (kT/e) : 1.6016281E-03 5.2015305E-02 energy calculations done at 7.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.780000 DelPhi exited at 06:21:08 7.782u 0.209s 0:08.29 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 Tue Oct 11 2011 at 06:21:08 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: 316 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2034 !!! WARNING: SEP 190 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.082370 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): 17.22400 63.72700 ymin,ymax (A): -3.557000 34.05600 zmin,zma (A): 18.83700 70.81000 x,y,z range (A): 46.50300 37.61300 51.97300 scale (grids/A): 3.082370 object centre (A): 40.47550 15.24950 44.82350 number of atom coordinates read : 2034 total number of charged atoms : 1950 net assigned charge : 6.025006 assigned positive charge : 318.1521 centred at (gu) : 93.03698 87.69646 89.79948 assigned negative charge : -312.1271 centred at (gu) : 93.71828 87.95907 89.85034 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 160508 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17757 grid for indexing accessible points = 1.400000 m= 85418 mr = 117352 m= 33780 mr = 70400 m= 9304 mr = 27334 m= 1717 mr = 7113 m= 179 mr = 1224 m= 4 mr = 93 m= 0 mr = 2 time to grow re-entrant surface = 0.5500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.050000 number of dielectric boundary points 67392 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.140000 number of grid points assigned charge 15600 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) : 2.054913 object centre at (A) : 40.47550 15.24950 44.82350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3679194 0.3097255 midg,1,midg; midg,igrid,midg 0.2377070 -4.8629958E-02 1,midg,midg; igrid,midg,midg 0.2082087 0.2419804 gauss-seidel spectral radius is 0.9992846 estimated iterations to convergence 295 setup time was (sec) 1.290000 now iterating at: 06:21:09 rms-change max change #iterations 9.955398 349.2150 at 10iterations 5.877431 130.3505 at 20iterations 3.464750 71.25798 at 30iterations 2.032789 38.69382 at 40iterations 1.189271 23.31886 at 50iterations 0.6964417 12.98356 at 60iterations 0.4067782 7.887138 at 70iterations 0.2367503 4.483557 at 80iterations 0.1385787 2.462242 at 90iterations 8.0714509E-02 1.899406 at 100iterations 4.6999667E-02 0.8345919 at 110iterations 2.7436797E-02 0.5503328 at 120iterations 1.6008932E-02 0.2843666 at 130iterations 9.3838489E-03 0.1708870 at 140iterations 5.5362508E-03 0.1068802 at 150iterations 3.3146248E-03 7.0007324E-02 at 160iterations 2.0219614E-03 4.1533470E-02 at 170iterations 1.2800432E-03 2.6565552E-02 at 180iterations finished qdiffx linear iterations at : 06:21:21 total time elapsed so far: 12.52000 # loops : 180 mean,max change (kT/e) : 1.2800432E-03 2.6565552E-02 energy calculations done at 12.52000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.69000 DelPhi exited at 06:21:21 12.690u 0.206s 0:13.43 95.9% 0+0k 0+0io 0pf+0w