Sat Oct 15 13:40:02 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 15 2011 at 13:40:03 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: 219 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2200 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: 0.6448575 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): -17.64200 29.58100 ymin,ymax (A): -3.786000 51.42000 zmin,zma (A): -24.69400 21.69800 x,y,z range (A): 47.22300 55.20600 46.39200 scale (grids/A): 0.6448575 object centre (A): 5.969500 23.81700 -1.498000 number of atom coordinates read : 2200 total number of charged atoms : 2062 net assigned charge : -1.999997 assigned positive charge : 333.7707 centred at (gu) : 90.65937 88.65571 90.46084 assigned negative charge : -335.7709 centred at (gu) : 90.86826 88.61175 90.54289 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 6290 nv = 96 ne = 84 npr = 42964 no. pairs analyzed = 42964 no. exposed pairs = 3057 no. arc points = 21908 no. surface atoms = 1021 nbur = 1179 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 335 mr = 3098 m= 3 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 17 time to turn everything in is 0.2700000 number of dielectric boundary points 3489 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2140 ## 214 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 7373 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.7157847E-09 -1.3798800E-08 midg,1,midg; midg,igrid,midg -1.0755678E-08 1.4739862E-09 1,midg,midg; igrid,midg,midg 1.7704414E-08 -3.1746502E-08 gauss-seidel spectral radius is 0.9875131 estimated iterations to convergence 73 setup time was (sec) 0.5700000 now iterating at: 13:40:04 rms-change max change #iterations 0.1398606 21.37135 at 10iterations 1.4109047E-02 2.137796 at 20iterations 1.4030967E-03 0.2497392 at 30iterations 1.4422841E-04 2.3708344E-02 at 40iterations 1.5248539E-05 2.8634071E-03 at 50iterations finished qdiffx linear iterations at : 13:40:09 total time elapsed so far: 5.050000 # loops : 50 mean,max change (kT/e) : 1.5248539E-05 2.8634071E-03 energy calculations done at 5.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.230000 DelPhi exited at 13:40:09 5.231u 0.501s 0:06.70 85.5% 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 15 2011 at 13:40:09 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: 219 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2200 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: 1.934572 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): -17.64200 29.58100 ymin,ymax (A): -3.786000 51.42000 zmin,zma (A): -24.69400 21.69800 x,y,z range (A): 47.22300 55.20600 46.39200 scale (grids/A): 1.934572 object centre (A): 5.969500 23.81700 -1.498000 number of atom coordinates read : 2200 total number of charged atoms : 2062 net assigned charge : -1.999997 assigned positive charge : 333.7707 centred at (gu) : 91.97797 85.96709 91.38232 assigned negative charge : -335.7709 centred at (gu) : 92.60460 85.83516 91.62870 start vw surface at 0.1100000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 66867 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21908 grid for indexing accessible points = 1.400000 m= 22859 mr = 43691 m= 3758 mr = 15709 m= 248 mr = 2155 m= 2 mr = 92 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 996 time to turn everything in is 0.5900000 number of dielectric boundary points 32087 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 160 iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 16258 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) : 0.6448575 object centre at (A) : 5.969500 23.81700 -1.498000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.0798408E-03 -8.7302765E-03 midg,1,midg; midg,igrid,midg -7.5290701E-03 2.1051411E-02 1,midg,midg; igrid,midg,midg 1.3515798E-02 -1.8857813E-02 gauss-seidel spectral radius is 0.9986515 estimated iterations to convergence 216 setup time was (sec) 0.9300000 now iterating at: 13:40:11 rms-change max change #iterations 4.066289 173.5147 at 10iterations 1.902700 66.27926 at 20iterations 0.8919997 34.40918 at 30iterations 0.4186437 14.45626 at 40iterations 0.1958960 6.949137 at 50iterations 9.1771871E-02 3.298441 at 60iterations 4.3033198E-02 1.381203 at 70iterations 2.0295003E-02 0.7219248 at 80iterations 9.4849225E-03 0.3347413 at 90iterations 4.4736639E-03 0.1643028 at 100iterations 2.1043431E-03 7.7615738E-02 at 110iterations 9.8503300E-04 3.5171509E-02 at 120iterations finished qdiffx linear iterations at : 13:40:23 total time elapsed so far: 12.36000 # loops : 120 mean,max change (kT/e) : 9.8503300E-04 3.5171509E-02 energy calculations done at 12.36000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.54000 DelPhi exited at 13:40:23 12.544u 0.534s 0:14.02 93.2% 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 15 2011 at 13:40:23 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: 219 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2200 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: 2.901859 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): -17.64200 29.58100 ymin,ymax (A): -3.786000 51.42000 zmin,zma (A): -24.69400 21.69800 x,y,z range (A): 47.22300 55.20600 46.39200 scale (grids/A): 2.901859 object centre (A): 5.969500 23.81700 -1.498000 number of atom coordinates read : 2200 total number of charged atoms : 2062 net assigned charge : -1.999997 assigned positive charge : 333.7707 centred at (gu) : 92.96700 83.95044 92.07334 assigned negative charge : -335.7709 centred at (gu) : 93.90685 83.75277 92.44311 start vw surface at 0.1300000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 154686 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21908 grid for indexing accessible points = 1.400000 m= 73723 mr = 107071 m= 26674 mr = 57669 m= 6583 mr = 20300 m= 949 mr = 4628 m= 77 mr = 612 m= 2 mr = 45 m= 0 mr = 0 time to grow re-entrant surface = 0.9200000 no. cavity mid-points inaccessible to solvent = 3248 time to turn everything in is 1.560000 number of dielectric boundary points 72369 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.730000 number of grid points assigned charge 16494 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) : 1.934572 object centre at (A) : 5.969500 23.81700 -1.498000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.9816714E-02 3.2017309E-02 midg,1,midg; midg,igrid,midg -0.2273914 0.3740193 1,midg,midg; igrid,midg,midg 9.5973872E-02 -0.1276715 gauss-seidel spectral radius is 0.9992803 estimated iterations to convergence 294 setup time was (sec) 1.950000 now iterating at: 13:40:26 rms-change max change #iterations 9.867838 442.1860 at 10iterations 5.922715 132.8413 at 20iterations 3.506663 85.32710 at 30iterations 2.061610 43.25983 at 40iterations 1.207909 26.18568 at 50iterations 0.7055451 13.74024 at 60iterations 0.4111589 8.199963 at 70iterations 0.2396500 4.968792 at 80iterations 0.1389131 2.772552 at 90iterations 8.0636822E-02 1.690209 at 100iterations 4.6687778E-02 0.8774314 at 110iterations 2.7099287E-02 0.5090448 at 120iterations 1.5679790E-02 0.2698307 at 130iterations 9.0966932E-03 0.1674767 at 140iterations 5.2530691E-03 9.6580505E-02 at 150iterations 3.0473096E-03 6.2468767E-02 at 160iterations 1.7661992E-03 3.3363342E-02 at 170iterations 1.0245597E-03 1.9546509E-02 at 180iterations finished qdiffx linear iterations at : 13:40:50 total time elapsed so far: 20.88000 # loops : 180 mean,max change (kT/e) : 1.0245597E-03 1.9546509E-02 energy calculations done at 20.88000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.11000 DelPhi exited at 13:40:51 21.118u 0.596s 0:28.04 77.3% 0+0k 0+0io 0pf+0w