Sat Oct 8 12:13:27 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 Sat Oct 8 2011 at 12:13:27 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 = 2477 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6463795 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): -24.56400 30.51200 ymin,ymax (A): -5.296000 39.90100 zmin,zma (A): 8.447001 50.83800 x,y,z range (A): 55.07600 45.19700 42.39100 scale (grids/A): 0.6463795 object centre (A): 2.973999 17.30250 29.64250 number of atom coordinates read : 2477 total number of charged atoms : 2337 net assigned charge : -1.999994 assigned positive charge : 376.0463 centred at (gu) : 89.88245 89.28831 91.02937 assigned negative charge : -378.0467 centred at (gu) : 90.00230 89.15354 91.04789 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6903 nv = 96 ne = 84 npr = 50729 no. pairs analyzed = 50729 no. exposed pairs = 2903 no. arc points = 21163 no. surface atoms = 975 nbur = 1502 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 339 mr = 3833 m= 2 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 63 time to turn everything in is 0.2900000 number of dielectric boundary points 3370 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2031 ## 195 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8227 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.8930278E-10 -7.2177624E-09 midg,1,midg; midg,igrid,midg -2.5344180E-08 1.2492903E-08 1,midg,midg; igrid,midg,midg 1.2965010E-08 -1.9183071E-08 gauss-seidel spectral radius is 0.9875863 estimated iterations to convergence 73 setup time was (sec) 0.5500000 now iterating at: 12:13:28 rms-change max change #iterations 0.1498262 23.78050 at 10iterations 1.5230514E-02 2.016396 at 20iterations 1.5386133E-03 0.2375069 at 30iterations 1.5479427E-04 2.4132252E-02 at 40iterations 1.5861637E-05 2.1495819E-03 at 50iterations finished qdiffx linear iterations at : 12:13:31 total time elapsed so far: 4.040000 # loops : 50 mean,max change (kT/e) : 1.5861637E-05 2.1495819E-03 energy calculations done at 4.040000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.200000 DelPhi exited at 12:13:32 4.208u 0.256s 0:04.79 92.9% 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 Sat Oct 8 2011 at 12:13:32 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 = 2477 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.939139 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): -24.56400 30.51200 ymin,ymax (A): -5.296000 39.90100 zmin,zma (A): 8.447001 50.83800 x,y,z range (A): 55.07600 45.19700 42.39100 scale (grids/A): 1.939139 object centre (A): 2.973999 17.30250 29.64250 number of atom coordinates read : 2477 total number of charged atoms : 2337 net assigned charge : -1.999994 assigned positive charge : 376.0463 centred at (gu) : 89.64709 87.86462 93.08800 assigned negative charge : -378.0467 centred at (gu) : 90.00671 87.46037 93.14339 start vw surface at 0.1300000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 74450 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21163 grid for indexing accessible points = 1.400000 m= 25946 mr = 51886 m= 4315 mr = 19173 m= 339 mr = 2828 m= 5 mr = 151 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 1634 time to turn everything in is 0.5300000 number of dielectric boundary points 31017 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 126 iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 18412 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) : 0.6463795 object centre at (A) : 2.973999 17.30250 29.64250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.9063638E-03 -1.7331153E-02 midg,1,midg; midg,igrid,midg -1.9365519E-02 4.3638167E-03 1,midg,midg; igrid,midg,midg 2.5372868E-02 -5.2138392E-02 gauss-seidel spectral radius is 0.9986672 estimated iterations to convergence 217 setup time was (sec) 0.8600000 now iterating at: 12:13:33 rms-change max change #iterations 4.317473 175.8374 at 10iterations 2.035460 71.91930 at 20iterations 0.9631491 32.49982 at 30iterations 0.4548892 15.31283 at 40iterations 0.2146307 6.977786 at 50iterations 0.1012767 3.096680 at 60iterations 4.7803123E-02 1.667702 at 70iterations 2.2618426E-02 0.6700630 at 80iterations 1.0688527E-02 0.3774948 at 90iterations 5.0478717E-03 0.1491499 at 100iterations 2.3922331E-03 7.9323769E-02 at 110iterations 1.1297171E-03 3.3586502E-02 at 120iterations finished qdiffx linear iterations at : 12:13:41 total time elapsed so far: 9.430000 # loops : 120 mean,max change (kT/e) : 1.1297171E-03 3.3586502E-02 energy calculations done at 9.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.620000 DelPhi exited at 12:13:42 9.622u 0.283s 0:10.22 96.8% 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 Sat Oct 8 2011 at 12:13:42 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 = 2477 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.908708 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): -24.56400 30.51200 ymin,ymax (A): -5.296000 39.90100 zmin,zma (A): 8.447001 50.83800 x,y,z range (A): 55.07600 45.19700 42.39100 scale (grids/A): 2.908708 object centre (A): 2.973999 17.30250 29.64250 number of atom coordinates read : 2477 total number of charged atoms : 2337 net assigned charge : -1.999994 assigned positive charge : 376.0463 centred at (gu) : 89.47054 86.79684 94.63198 assigned negative charge : -378.0467 centred at (gu) : 90.01009 86.19053 94.71501 start vw surface at 0.1200000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 172606 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21163 grid for indexing accessible points = 1.400000 m= 84855 mr = 125925 m= 30248 mr = 69754 m= 7790 mr = 24339 m= 1394 mr = 5950 m= 106 mr = 1029 m= 1 mr = 51 m= 0 mr = 0 time to grow re-entrant surface = 0.8200000 no. cavity mid-points inaccessible to solvent = 5270 time to turn everything in is 1.390000 number of dielectric boundary points 69952 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.540000 number of grid points assigned charge 18694 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) : 1.939139 object centre at (A) : 2.973999 17.30250 29.64250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.4201834E-02 -0.2895772 midg,1,midg; midg,igrid,midg -0.1996480 -1.1706906E-02 1,midg,midg; igrid,midg,midg 0.2736052 -0.7563223 gauss-seidel spectral radius is 0.9992621 estimated iterations to convergence 291 setup time was (sec) 1.750000 now iterating at: 12:13:44 rms-change max change #iterations 9.900035 396.5745 at 10iterations 5.731509 120.4733 at 20iterations 3.300122 71.02841 at 30iterations 1.897604 37.62755 at 40iterations 1.092873 19.40152 at 50iterations 0.6276655 11.32628 at 60iterations 0.3606105 6.298970 at 70iterations 0.2074857 4.182445 at 80iterations 0.1188662 2.170826 at 90iterations 6.8355538E-02 1.220075 at 100iterations 3.9212007E-02 0.7709169 at 110iterations 2.2515349E-02 0.4137416 at 120iterations 1.2912361E-02 0.2264338 at 130iterations 7.4051572E-03 0.1399488 at 140iterations 4.2568622E-03 7.5841904E-02 at 150iterations 2.4478834E-03 5.0458431E-02 at 160iterations 1.4050385E-03 2.4759293E-02 at 170iterations 8.0598082E-04 1.3757706E-02 at 180iterations finished qdiffx linear iterations at : 12:13:58 total time elapsed so far: 15.46000 # loops : 180 mean,max change (kT/e) : 8.0598082E-04 1.3757706E-02 energy calculations done at 15.46000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.64000 DelPhi exited at 12:13:58 15.646u 0.294s 0:16.23 98.1% 0+0k 0+0io 0pf+0w