Wed Dec 28 11:03:29 PST 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 Wed Dec 28 2011 at 11:03:29 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1957 !!! WARNING: ASH 125 has a net charge of -0.3190 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: 0.6482628 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): -5.350000 34.70100 ymin,ymax (A): -3.375000 49.45700 zmin,zma (A): -8.035000 46.88100 x,y,z range (A): 40.05100 52.83200 54.91600 scale (grids/A): 0.6482628 object centre (A): 14.67550 23.04100 19.42300 number of atom coordinates read : 1957 total number of charged atoms : 1824 net assigned charge : 4.681009 assigned positive charge : 291.7480 centred at (gu) : 89.41682 92.06538 89.99845 assigned negative charge : -287.0673 centred at (gu) : 89.32101 92.19044 90.05101 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 5626 nv = 96 ne = 84 npr = 40523 no. pairs analyzed = 40523 no. exposed pairs = 2511 no. arc points = 17615 no. surface atoms = 850 nbur = 1107 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 273 mr = 3101 m= 1 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 5 time to turn everything in is 0.3700000 number of dielectric boundary points 2773 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1822 ## 203 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 6604 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4572443E-08 3.3031127E-09 midg,1,midg; midg,igrid,midg 1.4425982E-08 -7.5909901E-09 1,midg,midg; igrid,midg,midg -1.6632873E-09 1.6927450E-08 gauss-seidel spectral radius is 0.9876130 estimated iterations to convergence 73 setup time was (sec) 0.8000000 now iterating at: 11:03:30 rms-change max change #iterations 0.1368560 27.65212 at 10iterations 1.3619681E-02 2.137409 at 20iterations 1.4050313E-03 0.2068710 at 30iterations 1.3945386E-04 2.3700714E-02 at 40iterations 1.3916983E-05 2.3279190E-03 at 50iterations finished qdiffx linear iterations at : 11:03:36 total time elapsed so far: 7.070000 # loops : 50 mean,max change (kT/e) : 1.3916983E-05 2.3279190E-03 energy calculations done at 7.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.290000 DelPhi exited at 11:03:37 7.290u 0.693s 0:08.43 94.6% 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 Wed Dec 28 2011 at 11:03:37 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1957 !!! WARNING: ASH 125 has a net charge of -0.3190 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: 1.944788 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): -5.350000 34.70100 ymin,ymax (A): -3.375000 49.45700 zmin,zma (A): -8.035000 46.88100 x,y,z range (A): 40.05100 52.83200 54.91600 scale (grids/A): 1.944788 object centre (A): 14.67550 23.04100 19.42300 number of atom coordinates read : 1957 total number of charged atoms : 1824 net assigned charge : 4.681009 assigned positive charge : 291.7480 centred at (gu) : 88.25048 96.19616 89.99533 assigned negative charge : -287.0673 centred at (gu) : 87.96311 96.57169 90.15309 start vw surface at 0.1400000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 60441 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17615 grid for indexing accessible points = 1.400000 m= 21457 mr = 41322 m= 3016 mr = 16157 m= 141 mr = 1956 m= 3 mr = 47 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 1108 time to turn everything in is 0.6500000 number of dielectric boundary points 25576 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 127 iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 14390 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) : 0.6482628 object centre at (A) : 14.67550 23.04100 19.42300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.4014854E-02 4.2106777E-02 midg,1,midg; midg,igrid,midg 3.5087410E-02 -5.5499417E-03 1,midg,midg; igrid,midg,midg 7.7902456E-03 1.0100137E-02 gauss-seidel spectral radius is 0.9986131 estimated iterations to convergence 213 setup time was (sec) 1.050000 now iterating at: 11:03:39 rms-change max change #iterations 3.791186 193.4869 at 10iterations 1.767062 62.15751 at 20iterations 0.8220525 31.59218 at 30iterations 0.3826753 13.59448 at 40iterations 0.1778633 6.124823 at 50iterations 8.2605198E-02 2.877773 at 60iterations 3.8435724E-02 1.311110 at 70iterations 1.7944930E-02 0.6117206 at 80iterations 8.3061112E-03 0.2899978 at 90iterations 3.8706257E-03 0.1417279 at 100iterations 1.7920345E-03 6.2875926E-02 at 110iterations 8.3849835E-04 3.1997204E-02 at 120iterations finished qdiffx linear iterations at : 11:03:55 total time elapsed so far: 17.81000 # loops : 120 mean,max change (kT/e) : 8.3849835E-04 3.1997204E-02 energy calculations done at 17.81000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.03000 DelPhi exited at 11:03:56 18.030u 0.578s 0:18.96 98.1% 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 Wed Dec 28 2011 at 11:03:56 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1957 !!! WARNING: ASH 125 has a net charge of -0.3190 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: 2.917183 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): -5.350000 34.70100 ymin,ymax (A): -3.375000 49.45700 zmin,zma (A): -8.035000 46.88100 x,y,z range (A): 40.05100 52.83200 54.91600 scale (grids/A): 2.917183 object centre (A): 14.67550 23.04100 19.42300 number of atom coordinates read : 1957 total number of charged atoms : 1824 net assigned charge : 4.681009 assigned positive charge : 291.7480 centred at (gu) : 87.37578 99.29409 89.99305 assigned negative charge : -287.0673 centred at (gu) : 86.94459 99.85755 90.22966 start vw surface at 0.1500000 fill in re-entrant regions at 0.6000000 boundary points on vw surface= 139475 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17615 grid for indexing accessible points = 1.400000 m= 69952 mr = 99892 m= 24680 mr = 57799 m= 5381 mr = 20264 m= 644 mr = 4065 m= 26 mr = 442 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 1.030000 no. cavity mid-points inaccessible to solvent = 3765 time to turn everything in is 1.800000 number of dielectric boundary points 57689 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 2.020000 number of grid points assigned charge 14587 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) : 1.944788 object centre at (A) : 14.67550 23.04100 19.42300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.5541858E-03 0.8558927 midg,1,midg; midg,igrid,midg 0.3576885 -0.1076761 1,midg,midg; igrid,midg,midg 0.1456047 7.0687205E-02 gauss-seidel spectral radius is 0.9992421 estimated iterations to convergence 287 setup time was (sec) 2.340000 now iterating at: 11:03:59 rms-change max change #iterations 8.850744 355.7548 at 10iterations 5.110095 137.0189 at 20iterations 2.919836 69.50754 at 30iterations 1.673154 47.26743 at 40iterations 0.9555591 20.29008 at 50iterations 0.5470524 12.21738 at 60iterations 0.3107572 6.643003 at 70iterations 0.1767576 3.861451 at 80iterations 0.1011365 2.323913 at 90iterations 5.7461113E-02 1.109612 at 100iterations 3.2744389E-02 0.6357079 at 110iterations 1.8653482E-02 0.3947563 at 120iterations 1.0631285E-02 0.2152634 at 130iterations 6.0668434E-03 0.1210952 at 140iterations 3.4535525E-03 7.0388794E-02 at 150iterations 1.9619798E-03 3.8203001E-02 at 160iterations 1.1216055E-03 2.2514343E-02 at 170iterations 6.3651812E-04 1.2216091E-02 at 180iterations finished qdiffx linear iterations at : 11:04:26 total time elapsed so far: 29.30000 # loops : 180 mean,max change (kT/e) : 6.3651812E-04 1.2216091E-02 energy calculations done at 29.30000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 29.53000 DelPhi exited at 11:04:27 29.537u 0.804s 0:30.76 98.6% 0+0k 0+0io 0pf+0w