Mon Oct 10 14:37:10 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 Mon Oct 10 2011 at 14:37:10 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2101 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: 0.7402787 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): -21.13600 24.22200 ymin,ymax (A): -7.883000 36.34500 zmin,zma (A): -3.386000 44.70400 x,y,z range (A): 45.35800 44.22800 48.09000 scale (grids/A): 0.7402787 object centre (A): 1.543000 14.23100 20.65900 number of atom coordinates read : 2101 total number of charged atoms : 1962 net assigned charge : -5.999980 assigned positive charge : 314.2619 centred at (gu) : 89.03547 90.36958 90.03917 assigned negative charge : -320.2620 centred at (gu) : 89.10034 90.45176 90.20709 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 8014 nv = 96 ne = 84 npr = 43393 no. pairs analyzed = 43393 no. exposed pairs = 2700 no. arc points = 18717 no. surface atoms = 911 nbur = 1190 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 534 mr = 4495 m= 3 mr = 106 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1800000 number of dielectric boundary points 3950 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1516 ## 137 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 8417 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.1936603E-08 -2.8284089E-07 midg,1,midg; midg,igrid,midg -2.1942077E-08 -2.0460263E-07 1,midg,midg; igrid,midg,midg -4.7338027E-08 -1.4500431E-07 gauss-seidel spectral radius is 0.9904903 estimated iterations to convergence 83 setup time was (sec) 0.3700000 now iterating at: 14:37:11 rms-change max change #iterations 0.2460990 30.20723 at 10iterations 3.2698676E-02 3.859856 at 20iterations 4.4339681E-03 0.5751305 at 30iterations 5.9936568E-04 7.8082561E-02 at 40iterations 8.0998405E-05 1.0261536E-02 at 50iterations finished qdiffx linear iterations at : 14:37:14 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 8.0998405E-05 1.0261536E-02 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.400000 DelPhi exited at 14:37:14 3.408u 0.170s 0:04.21 84.7% 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 Mon Oct 10 2011 at 14:37:14 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2101 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: 2.220836 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): -21.13600 24.22200 ymin,ymax (A): -7.883000 36.34500 zmin,zma (A): -3.386000 44.70400 x,y,z range (A): 45.35800 44.22800 48.09000 scale (grids/A): 2.220836 object centre (A): 1.543000 14.23100 20.65900 number of atom coordinates read : 2101 total number of charged atoms : 1962 net assigned charge : -5.999980 assigned positive charge : 314.2619 centred at (gu) : 87.10641 91.10866 90.11755 assigned negative charge : -320.2620 centred at (gu) : 87.30112 91.35510 90.62130 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 84151 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18717 grid for indexing accessible points = 1.400000 m= 33771 mr = 58691 m= 7186 mr = 25693 m= 786 mr = 4934 m= 35 mr = 413 m= 0 mr = 10 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4300000 number of dielectric boundary points 36188 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 54 iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 15633 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) : 0.7402787 object centre at (A) : 1.543000 14.23100 20.65900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.2478634E-02 -0.1408283 midg,1,midg; midg,igrid,midg -2.1332109E-02 -3.4683093E-02 1,midg,midg; igrid,midg,midg -5.2786921E-03 1.4401548E-02 gauss-seidel spectral radius is 0.9989250 estimated iterations to convergence 241 setup time was (sec) 0.6600000 now iterating at: 14:37:15 rms-change max change #iterations 5.088232 226.1356 at 10iterations 2.577022 85.23778 at 20iterations 1.313757 37.52301 at 30iterations 0.6672250 21.79647 at 40iterations 0.3404369 9.409391 at 50iterations 0.1734532 5.253613 at 60iterations 8.8481061E-02 2.659520 at 70iterations 4.5081548E-02 1.278009 at 80iterations 2.3020744E-02 0.6648111 at 90iterations 1.1717841E-02 0.3198311 at 100iterations 5.9907115E-03 0.1535339 at 110iterations 3.0460069E-03 8.4800720E-02 at 120iterations finished qdiffx linear iterations at : 14:37:22 total time elapsed so far: 7.860000 # loops : 120 mean,max change (kT/e) : 3.0460069E-03 8.4800720E-02 energy calculations done at 7.860000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.990000 DelPhi exited at 14:37:23 7.995u 0.196s 0:08.55 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 Mon Oct 10 2011 at 14:37:23 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2101 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: 3.331254 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): -21.13600 24.22200 ymin,ymax (A): -7.883000 36.34500 zmin,zma (A): -3.386000 44.70400 x,y,z range (A): 45.35800 44.22800 48.09000 scale (grids/A): 3.331254 object centre (A): 1.543000 14.23100 20.65900 number of atom coordinates read : 2101 total number of charged atoms : 1962 net assigned charge : -5.999980 assigned positive charge : 314.2619 centred at (gu) : 85.65956 91.66302 90.17622 assigned negative charge : -320.2620 centred at (gu) : 85.95181 92.03274 90.93188 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 193500 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18717 grid for indexing accessible points = 1.400000 m= 103853 mr = 140880 m= 44362 mr = 86580 m= 13871 mr = 36702 m= 3096 mr = 10960 m= 512 mr = 2330 m= 41 mr = 324 m= 1 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.6600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.320000 number of dielectric boundary points 81437 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.410000 number of grid points assigned charge 15696 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) : 2.220836 object centre at (A) : 1.543000 14.23100 20.65900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.9524928E-03 -1.428057 midg,1,midg; midg,igrid,midg -0.1952590 -0.1730725 1,midg,midg; igrid,midg,midg -0.1689042 0.2164004 gauss-seidel spectral radius is 0.9993185 estimated iterations to convergence 302 setup time was (sec) 1.550000 now iterating at: 14:37:25 rms-change max change #iterations 10.94866 419.6878 at 10iterations 6.445599 142.6934 at 20iterations 3.801401 64.26939 at 30iterations 2.230949 40.53146 at 40iterations 1.314544 23.79974 at 50iterations 0.7717900 13.65713 at 60iterations 0.4539713 7.245720 at 70iterations 0.2668667 4.451759 at 80iterations 0.1568483 3.191753 at 90iterations 9.2178240E-02 1.556999 at 100iterations 5.4124072E-02 0.8496857 at 110iterations 3.1768981E-02 0.5038619 at 120iterations 1.8646436E-02 0.3197818 at 130iterations 1.0958719E-02 0.1937008 at 140iterations 6.4326841E-03 0.1078777 at 150iterations 3.7739356E-03 6.5795898E-02 at 160iterations 2.2156283E-03 3.4057617E-02 at 170iterations 1.2996547E-03 2.0198822E-02 at 180iterations finished qdiffx linear iterations at : 14:37:36 total time elapsed so far: 13.02000 # loops : 180 mean,max change (kT/e) : 1.2996547E-03 2.0198822E-02 energy calculations done at 13.02000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.16000 DelPhi exited at 14:37:37 13.165u 0.210s 0:13.99 95.5% 0+0k 0+0io 0pf+0w