Sun Oct 9 18:13:21 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 18:13:21 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 = 2896 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5575306 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): -8.106999 55.74600 ymin,ymax (A): -14.41600 34.11600 zmin,zma (A): 22.50700 70.51300 x,y,z range (A): 63.85300 48.53200 48.00600 scale (grids/A): 0.5575306 object centre (A): 23.81950 9.850000 46.51000 number of atom coordinates read : 2896 total number of charged atoms : 2752 net assigned charge : 6.000026 assigned positive charge : 440.7544 centred at (gu) : 90.24503 90.66899 88.61488 assigned negative charge : -434.7553 centred at (gu) : 90.30072 90.75872 88.53857 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 5950 nv = 96 ne = 84 npr = 57168 no. pairs analyzed = 57168 no. exposed pairs = 3801 no. arc points = 26478 no. surface atoms = 1281 nbur = 1615 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 287 mr = 3042 m= 2 mr = 12 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 0.3400000 number of dielectric boundary points 3185 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2668 ## 323 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 7645 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.4087277E-10 9.6758601E-10 midg,1,midg; midg,igrid,midg 1.2585726E-09 -3.5542636E-10 1,midg,midg; igrid,midg,midg 1.0826579E-09 4.7539181E-11 gauss-seidel spectral radius is 0.9834018 estimated iterations to convergence 64 setup time was (sec) 0.5700000 now iterating at: 18:13:22 rms-change max change #iterations 7.7822186E-02 13.07374 at 10iterations 5.6169960E-03 0.9710083 at 20iterations 5.5744406E-04 8.5517883E-02 at 30iterations 1.5872366E-04 2.2008896E-02 at 40iterations 7.6455770E-05 1.1202335E-02 at 50iterations finished qdiffx linear iterations at : 18:13:25 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 7.6455770E-05 1.1202335E-02 energy calculations done at 3.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.440000 DelPhi exited at 18:13:25 3.443u 0.170s 0:04.02 89.8% 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 18:13:25 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 = 2896 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.672592 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): -8.106999 55.74600 ymin,ymax (A): -14.41600 34.11600 zmin,zma (A): 22.50700 70.51300 x,y,z range (A): 63.85300 48.53200 48.00600 scale (grids/A): 1.672592 object centre (A): 23.81950 9.850000 46.51000 number of atom coordinates read : 2896 total number of charged atoms : 2752 net assigned charge : 6.000026 assigned positive charge : 440.7544 centred at (gu) : 90.73418 92.00620 85.84372 assigned negative charge : -434.7553 centred at (gu) : 90.90195 92.27596 85.61546 start vw surface at 0.1800000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 65712 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26478 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 21706 mr = 44520 m= 2607 mr = 14710 m= 116 mr = 1301 m= 3 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5400000 number of dielectric boundary points 29599 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 234 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 21210 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) : 0.5575306 object centre at (A) : 23.81950 9.850000 46.51000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.7035312E-03 6.5443274E-03 midg,1,midg; midg,igrid,midg 9.9884989E-03 -8.0807572E-03 1,midg,midg; igrid,midg,midg 2.2997644E-02 -5.5251005E-03 gauss-seidel spectral radius is 0.9982646 estimated iterations to convergence 191 setup time was (sec) 0.8400000 now iterating at: 18:13:26 rms-change max change #iterations 3.503741 165.5171 at 10iterations 1.483610 55.96980 at 20iterations 0.6325804 22.38840 at 30iterations 0.2692330 9.075422 at 40iterations 0.1149439 4.118451 at 50iterations 4.9289923E-02 1.825583 at 60iterations 2.0988628E-02 0.7727127 at 70iterations 8.9664189E-03 0.3161469 at 80iterations 3.8611258E-03 0.1470995 at 90iterations 1.6824168E-03 6.2940598E-02 at 100iterations 7.6696259E-04 2.6966095E-02 at 110iterations 3.8898032E-04 1.3980031E-02 at 120iterations finished qdiffx linear iterations at : 18:13:33 total time elapsed so far: 7.430000 # loops : 120 mean,max change (kT/e) : 3.8898032E-04 1.3980031E-02 energy calculations done at 7.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.660000 DelPhi exited at 18:13:34 7.667u 0.188s 0:08.20 95.6% 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 Sun Oct 9 2011 at 18:13:34 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 = 2896 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.508888 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): -8.106999 55.74600 ymin,ymax (A): -14.41600 34.11600 zmin,zma (A): 22.50700 70.51300 x,y,z range (A): 63.85300 48.53200 48.00600 scale (grids/A): 2.508888 object centre (A): 23.81950 9.850000 46.51000 number of atom coordinates read : 2896 total number of charged atoms : 2752 net assigned charge : 6.000026 assigned positive charge : 440.7544 centred at (gu) : 91.10117 93.00900 83.76546 assigned negative charge : -434.7553 centred at (gu) : 91.35269 93.41390 83.42303 start vw surface at 0.1700000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 152328 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26478 grid for indexing accessible points = 1.400000 m= 73259 mr = 109058 m= 22699 mr = 57341 m= 4225 mr = 16873 m= 363 mr = 2684 m= 3 mr = 178 m= 0 mr = 0 time to grow re-entrant surface = 0.7300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.250000 number of dielectric boundary points 66743 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 13 iepsmp to db, and charging done at 1.410000 number of grid points assigned charge 22007 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) : 1.672592 object centre at (A) : 23.81950 9.850000 46.51000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.1658351E-02 7.5550333E-02 midg,1,midg; midg,igrid,midg 0.1584776 -0.1573560 1,midg,midg; igrid,midg,midg 0.8938155 -6.4375632E-02 gauss-seidel spectral radius is 0.9991621 estimated iterations to convergence 273 setup time was (sec) 1.580000 now iterating at: 18:13:35 rms-change max change #iterations 9.011488 324.6767 at 10iterations 5.154762 135.0293 at 20iterations 2.934713 72.64761 at 30iterations 1.653500 38.17838 at 40iterations 0.9318386 24.81594 at 50iterations 0.5219896 12.03623 at 60iterations 0.2928074 7.051250 at 70iterations 0.1639346 4.902438 at 80iterations 9.1564521E-02 2.112675 at 90iterations 5.1020592E-02 1.077799 at 100iterations 2.8487541E-02 0.7094860 at 110iterations 1.5872955E-02 0.3680120 at 120iterations 8.8523012E-03 0.2009759 at 130iterations 4.9351430E-03 0.1201706 at 140iterations 2.7502172E-03 5.7188034E-02 at 150iterations 1.5355386E-03 3.8112640E-02 at 160iterations 8.6160429E-04 1.8854618E-02 at 170iterations 4.8645429E-04 9.3669891E-03 at 180iterations finished qdiffx linear iterations at : 18:13:45 total time elapsed so far: 11.69000 # loops : 180 mean,max change (kT/e) : 4.8645429E-04 9.3669891E-03 energy calculations done at 11.69000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.90000 DelPhi exited at 18:13:46 11.906u 0.171s 0:12.36 97.6% 0+0k 0+0io 0pf+0w