Tue Oct 11 08:21:57 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 08:21:57 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1157 !!! WARNING: HIT 60 has a net charge of 0.5140 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: 0.7385126 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): -6.733000 30.13400 ymin,ymax (A): 1.167000 39.62300 zmin,zma (A): -2.006000 46.19900 x,y,z range (A): 36.86700 38.45600 48.20500 scale (grids/A): 0.7385126 object centre (A): 11.70050 20.39500 22.09650 number of atom coordinates read : 1157 total number of charged atoms : 1061 net assigned charge : 5.514003 assigned positive charge : 178.1651 centred at (gu) : 89.32063 89.37980 88.50612 assigned negative charge : -172.6512 centred at (gu) : 89.02979 89.35343 88.55440 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.0000000E-02 boundary points on vw surface= 4354 nv = 96 ne = 84 npr = 22184 no. pairs analyzed = 22184 no. exposed pairs = 1504 no. arc points = 11090 no. surface atoms = 508 nbur = 649 mkacc time = 3.9999999E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 261 mr = 2241 m= 2 mr = 50 m= 0 mr = 0 time to grow re-entrant surface = 4.9999997E-02 no. cavity mid-points inaccessible to solvent = 33 time to turn everything in is 0.1200000 number of dielectric boundary points 2326 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 959 ## 88 charges are in solution ## iepsmp to db, and charging done at 0.2000000 number of grid points assigned charge 4484 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.5868795E-07 5.3340379E-08 midg,1,midg; midg,igrid,midg 9.0455657E-08 9.7303548E-08 1,midg,midg; igrid,midg,midg -7.3405978E-08 2.1567385E-07 gauss-seidel spectral radius is 0.9903504 estimated iterations to convergence 83 setup time was (sec) 0.3300000 now iterating at: 08:21:57 rms-change max change #iterations 0.1815683 35.31109 at 10iterations 2.4057982E-02 4.028144 at 20iterations 3.1154931E-03 0.5301514 at 30iterations 4.2058711E-04 8.4331512E-02 at 40iterations 5.5657692E-05 8.5983276E-03 at 50iterations finished qdiffx linear iterations at : 08:22:00 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 5.5657692E-05 8.5983276E-03 energy calculations done at 3.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.340000 DelPhi exited at 08:22:01 3.345u 0.210s 0:04.12 86.1% 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 08:22:01 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1157 !!! WARNING: HIT 60 has a net charge of 0.5140 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: 2.215538 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): -6.733000 30.13400 ymin,ymax (A): 1.167000 39.62300 zmin,zma (A): -2.006000 46.19900 x,y,z range (A): 36.86700 38.45600 48.20500 scale (grids/A): 2.215538 object centre (A): 11.70050 20.39500 22.09650 number of atom coordinates read : 1157 total number of charged atoms : 1061 net assigned charge : 5.514003 assigned positive charge : 178.1651 centred at (gu) : 87.96193 88.13950 85.51865 assigned negative charge : -172.6512 centred at (gu) : 87.08964 88.06055 85.66325 start vw surface at 5.9999999E-02 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 45477 reading accessible surface arcs data from file ARCDAT no. of arc points read = 11090 grid for indexing accessible points = 1.400000 m= 17026 mr = 29582 m= 3153 mr = 12667 m= 298 mr = 2117 m= 20 mr = 196 m= 0 mr = 14 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 1005 time to turn everything in is 0.2400000 number of dielectric boundary points 21398 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 35 iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 8451 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) : 0.7385126 object centre at (A) : 11.70050 20.39500 22.09650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.4659456E-02 4.2188126E-03 midg,1,midg; midg,igrid,midg 3.7374984E-02 2.9229179E-02 1,midg,midg; igrid,midg,midg -2.7315166E-02 3.7521467E-02 gauss-seidel spectral radius is 0.9988307 estimated iterations to convergence 231 setup time was (sec) 0.4600000 now iterating at: 08:22:02 rms-change max change #iterations 3.658188 177.0108 at 10iterations 1.813620 78.85949 at 20iterations 0.8955252 33.81001 at 30iterations 0.4423250 18.60604 at 40iterations 0.2180227 7.753551 at 50iterations 0.1081957 4.025579 at 60iterations 5.3265981E-02 2.007002 at 70iterations 2.6200801E-02 1.028954 at 80iterations 1.3031570E-02 0.4873114 at 90iterations 6.4419550E-03 0.2500629 at 100iterations 3.1808065E-03 0.1265259 at 110iterations 1.5693832E-03 5.7661533E-02 at 120iterations finished qdiffx linear iterations at : 08:22:09 total time elapsed so far: 7.460000 # loops : 120 mean,max change (kT/e) : 1.5693832E-03 5.7661533E-02 energy calculations done at 7.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.610000 DelPhi exited at 08:22:09 7.608u 0.217s 0:08.16 95.7% 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 08:22:09 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1157 !!! WARNING: HIT 60 has a net charge of 0.5140 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: 3.323307 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): -6.733000 30.13400 ymin,ymax (A): 1.167000 39.62300 zmin,zma (A): -2.006000 46.19900 x,y,z range (A): 36.86700 38.45600 48.20500 scale (grids/A): 3.323307 object centre (A): 11.70050 20.39500 22.09650 number of atom coordinates read : 1157 total number of charged atoms : 1061 net assigned charge : 5.514003 assigned positive charge : 178.1651 centred at (gu) : 86.94296 87.20921 83.27803 assigned negative charge : -172.6512 centred at (gu) : 85.63449 87.09089 83.49489 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 104661 reading accessible surface arcs data from file ARCDAT no. of arc points read = 11090 grid for indexing accessible points = 1.400000 m= 52717 mr = 71479 m= 21273 mr = 43008 m= 5906 mr = 17436 m= 1177 mr = 4619 m= 190 mr = 917 m= 19 mr = 145 m= 0 mr = 18 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 3312 time to turn everything in is 0.7200000 number of dielectric boundary points 48321 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 8488 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) : 2.215538 object centre at (A) : 11.70050 20.39500 22.09650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3617914 2.2389138E-02 midg,1,midg; midg,igrid,midg 0.3285861 0.2399433 1,midg,midg; igrid,midg,midg -0.2229080 0.2649996 gauss-seidel spectral radius is 0.9992895 estimated iterations to convergence 296 setup time was (sec) 0.9600000 now iterating at: 08:22:10 rms-change max change #iterations 7.988907 304.4895 at 10iterations 4.652017 119.9727 at 20iterations 2.688560 68.73120 at 30iterations 1.550220 34.26820 at 40iterations 0.9005016 19.45507 at 50iterations 0.5201188 10.70944 at 60iterations 0.3010187 7.400234 at 70iterations 0.1741793 3.772709 at 80iterations 0.1005049 2.073742 at 90iterations 5.8214851E-02 1.288147 at 100iterations 3.3758234E-02 0.7044187 at 110iterations 1.9586630E-02 0.4191194 at 120iterations 1.1297680E-02 0.2327385 at 130iterations 6.5507488E-03 0.1549942 at 140iterations 3.7854169E-03 8.3896637E-02 at 150iterations 2.1969944E-03 4.8233032E-02 at 160iterations 1.2715250E-03 2.5726318E-02 at 170iterations 7.3611236E-04 1.5045166E-02 at 180iterations finished qdiffx linear iterations at : 08:22:22 total time elapsed so far: 12.09000 # loops : 180 mean,max change (kT/e) : 7.3611236E-04 1.5045166E-02 energy calculations done at 12.09000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.22000 DelPhi exited at 08:22:22 12.226u 0.221s 0:13.14 94.6% 0+0k 0+0io 0pf+0w