Sat Oct 8 18:27:19 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 Sat Oct 8 2011 at 18:27:19 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3197 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: 0.5943437 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): 50.12600 109.6160 ymin,ymax (A): -18.85800 41.04000 zmin,zma (A): -34.90400 24.35600 x,y,z range (A): 59.49000 59.89800 59.26000 scale (grids/A): 0.5943437 object centre (A): 79.87100 11.09100 -5.274002 number of atom coordinates read : 3197 total number of charged atoms : 3056 net assigned charge : 5.500037 assigned positive charge : 476.8068 centred at (gu) : 88.42413 89.64600 91.49035 assigned negative charge : -471.3080 centred at (gu) : 88.36101 89.79694 91.46423 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7759 nv = 96 ne = 84 npr = 63344 no. pairs analyzed = 63344 no. exposed pairs = 4304 no. arc points = 30473 no. surface atoms = 1423 nbur = 1774 mkacc time = 0.1400000 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 = 1.456000 m= 411 mr = 3990 m= 4 mr = 35 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 4149 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3012 ## 304 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 9569 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.2329442E-10 4.0923736E-09 midg,1,midg; midg,igrid,midg 8.0625187E-09 -3.4166090E-09 1,midg,midg; igrid,midg,midg -6.2425953E-10 2.9909286E-09 gauss-seidel spectral radius is 0.9854126 estimated iterations to convergence 68 setup time was (sec) 0.5900000 now iterating at: 18:27:20 rms-change max change #iterations 0.1181257 19.37357 at 10iterations 1.0672072E-02 1.676435 at 20iterations 1.7299841E-03 0.2755127 at 30iterations 5.0634873E-04 8.3393097E-02 at 40iterations 1.6463833E-04 2.7053833E-02 at 50iterations finished qdiffx linear iterations at : 18:27:22 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 1.6463833E-04 2.7053833E-02 energy calculations done at 3.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.430000 DelPhi exited at 18:27:23 3.435u 0.192s 0:03.91 92.5% 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 18:27:23 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3197 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.783031 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): 50.12600 109.6160 ymin,ymax (A): -18.85800 41.04000 zmin,zma (A): -34.90400 24.35600 x,y,z range (A): 59.49000 59.89800 59.26000 scale (grids/A): 1.783031 object centre (A): 79.87100 11.09100 -5.274002 number of atom coordinates read : 3197 total number of charged atoms : 3056 net assigned charge : 5.500037 assigned positive charge : 476.8068 centred at (gu) : 85.27132 88.93705 94.47021 assigned negative charge : -471.3080 centred at (gu) : 85.08255 89.39074 94.39214 start vw surface at 0.1800000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 83640 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30473 grid for indexing accessible points = 1.400000 m= 29742 mr = 56159 m= 4506 mr = 20975 m= 220 mr = 2564 m= 4 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 96 time to turn everything in is 0.6200000 number of dielectric boundary points 38384 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 243 iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 23883 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) : 0.5943437 object centre at (A) : 79.87100 11.09100 -5.274002 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0231183E-02 3.0802526E-02 midg,1,midg; midg,igrid,midg 2.3136087E-02 -1.3316447E-02 1,midg,midg; igrid,midg,midg 1.8730239E-03 4.6351631E-03 gauss-seidel spectral radius is 0.9985172 estimated iterations to convergence 206 setup time was (sec) 0.9100000 now iterating at: 18:27:24 rms-change max change #iterations 4.140913 150.5004 at 10iterations 1.864058 63.13655 at 20iterations 0.8437536 30.11668 at 30iterations 0.3834885 12.23174 at 40iterations 0.1740991 5.350846 at 50iterations 7.9328388E-02 2.569557 at 60iterations 3.6315970E-02 1.141840 at 70iterations 1.6820909E-02 0.4843369 at 80iterations 7.9872413E-03 0.2633781 at 90iterations 3.9947969E-03 0.1375504 at 100iterations 2.1469661E-03 8.2412720E-02 at 110iterations 1.2576921E-03 4.7225952E-02 at 120iterations finished qdiffx linear iterations at : 18:27:31 total time elapsed so far: 7.590000 # loops : 120 mean,max change (kT/e) : 1.2576921E-03 4.7225952E-02 energy calculations done at 7.590000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.780000 DelPhi exited at 18:27:31 7.781u 0.218s 0:08.29 96.3% 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 18:27:31 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3197 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.674547 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): 50.12600 109.6160 ymin,ymax (A): -18.85800 41.04000 zmin,zma (A): -34.90400 24.35600 x,y,z range (A): 59.49000 59.89800 59.26000 scale (grids/A): 2.674547 object centre (A): 79.87100 11.09100 -5.274002 number of atom coordinates read : 3197 total number of charged atoms : 3056 net assigned charge : 5.500037 assigned positive charge : 476.8068 centred at (gu) : 82.90674 88.40540 96.70513 assigned negative charge : -471.3080 centred at (gu) : 82.62370 89.08582 96.58820 start vw surface at 0.1500000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 193690 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30473 grid for indexing accessible points = 1.400000 m= 96199 mr = 137344 m= 34369 mr = 76475 m= 7853 mr = 26609 m= 882 mr = 5540 m= 33 mr = 459 m= 2 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.9100000 no. cavity mid-points inaccessible to solvent = 284 time to turn everything in is 1.530000 number of dielectric boundary points 86601 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.690000 number of grid points assigned charge 24447 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) : 1.783031 object centre at (A) : 79.87100 11.09100 -5.274002 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1316464 0.2056950 midg,1,midg; midg,igrid,midg 0.3296376 -0.1995316 1,midg,midg; igrid,midg,midg 0.3415202 -1.9293256E-02 gauss-seidel spectral radius is 0.9992468 estimated iterations to convergence 288 setup time was (sec) 1.870000 now iterating at: 18:27:33 rms-change max change #iterations 10.33725 360.6194 at 10iterations 6.160826 145.1549 at 20iterations 3.631193 85.51834 at 30iterations 2.125312 57.87566 at 40iterations 1.239972 23.86255 at 50iterations 0.7205086 16.19312 at 60iterations 0.4170572 8.004332 at 70iterations 0.2401342 4.375835 at 80iterations 0.1386382 2.689209 at 90iterations 7.9760075E-02 1.421379 at 100iterations 4.6000425E-02 0.7987843 at 110iterations 2.6549023E-02 0.4857407 at 120iterations 1.5325240E-02 0.2838078 at 130iterations 8.8841757E-03 0.1682892 at 140iterations 5.2083498E-03 9.6294403E-02 at 150iterations 3.1092004E-03 6.1721802E-02 at 160iterations 1.9122352E-03 4.1038513E-02 at 170iterations 1.2344214E-03 2.5634766E-02 at 180iterations finished qdiffx linear iterations at : 18:27:44 total time elapsed so far: 12.71000 # loops : 180 mean,max change (kT/e) : 1.2344214E-03 2.5634766E-02 energy calculations done at 12.71000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.88000 DelPhi exited at 18:27:45 12.887u 0.225s 0:13.41 97.6% 0+0k 0+0io 0pf+0w