Mon Oct 10 14:09:45 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 14:09:45 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2642 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: 0.6323043 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): 3.013000 58.63000 ymin,ymax (A): 4.969000 61.27100 zmin,zma (A): 6.583000 53.94300 x,y,z range (A): 55.61700 56.30200 47.36000 scale (grids/A): 0.6323043 object centre (A): 30.82150 33.12000 30.26300 number of atom coordinates read : 2642 total number of charged atoms : 2469 net assigned charge : 5.500015 assigned positive charge : 395.1147 centred at (gu) : 90.53054 89.94516 91.71605 assigned negative charge : -389.6153 centred at (gu) : 90.55732 89.90697 91.68353 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 7232 nv = 96 ne = 84 npr = 51835 no. pairs analyzed = 51835 no. exposed pairs = 3632 no. arc points = 26001 no. surface atoms = 1198 nbur = 1444 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 402 mr = 3774 m= 4 mr = 44 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 3820 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2505 ## 265 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 8603 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.3290037E-09 1.3592901E-08 midg,1,midg; midg,igrid,midg 2.7482212E-09 9.8163140E-09 1,midg,midg; igrid,midg,midg 7.9213951E-09 4.2338684E-09 gauss-seidel spectral radius is 0.9870551 estimated iterations to convergence 72 setup time was (sec) 0.6100000 now iterating at: 14:09:46 rms-change max change #iterations 0.1388577 21.60456 at 10iterations 1.3263609E-02 2.188084 at 20iterations 1.2607288E-03 0.1757813 at 30iterations 1.2406163E-04 1.8698692E-02 at 40iterations 1.2396674E-05 1.7662048E-03 at 50iterations finished qdiffx linear iterations at : 14:09:50 total time elapsed so far: 4.310000 # loops : 50 mean,max change (kT/e) : 1.2396674E-05 1.7662048E-03 energy calculations done at 4.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.480000 DelPhi exited at 14:09:50 4.485u 0.403s 0:05.20 93.8% 0+0k 0+0io 5pf+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 14:09:50 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2642 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: 1.896913 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): 3.013000 58.63000 ymin,ymax (A): 4.969000 61.27100 zmin,zma (A): 6.583000 53.94300 x,y,z range (A): 55.61700 56.30200 47.36000 scale (grids/A): 1.896913 object centre (A): 30.82150 33.12000 30.26300 number of atom coordinates read : 2642 total number of charged atoms : 2469 net assigned charge : 5.500015 assigned positive charge : 395.1147 centred at (gu) : 91.59069 89.83504 95.14718 assigned negative charge : -389.6153 centred at (gu) : 91.67146 89.72060 95.05010 start vw surface at 0.1100000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 77822 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26001 grid for indexing accessible points = 1.400000 m= 27238 mr = 52294 m= 4022 mr = 19031 m= 248 mr = 2246 m= 5 mr = 81 m= 0 mr = 0 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 84 time to turn everything in is 0.6400000 number of dielectric boundary points 35683 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 206 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 19432 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) : 0.6323043 object centre at (A) : 30.82150 33.12000 30.26300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.2511304E-02 3.4049373E-02 midg,1,midg; midg,igrid,midg 8.9027490E-03 1.2798051E-03 1,midg,midg; igrid,midg,midg 7.5110970E-03 -8.2219364E-03 gauss-seidel spectral radius is 0.9986361 estimated iterations to convergence 215 setup time was (sec) 0.9500000 now iterating at: 14:09:52 rms-change max change #iterations 4.239787 191.3064 at 10iterations 1.980048 76.03696 at 20iterations 0.9260092 28.47304 at 30iterations 0.4342490 13.71664 at 40iterations 0.2025922 6.855923 at 50iterations 9.4852455E-02 3.037311 at 60iterations 4.4380218E-02 1.382187 at 70iterations 2.0808699E-02 0.6536732 at 80iterations 9.7684534E-03 0.3011856 at 90iterations 4.5585977E-03 0.1506748 at 100iterations 2.1313799E-03 6.8754196E-02 at 110iterations 9.9686219E-04 3.0942917E-02 at 120iterations finished qdiffx linear iterations at : 14:10:01 total time elapsed so far: 10.51000 # loops : 120 mean,max change (kT/e) : 9.9686219E-04 3.0942917E-02 energy calculations done at 10.51000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.68000 DelPhi exited at 14:10:02 10.683u 0.443s 0:11.73 94.7% 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 14:10:02 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2642 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: 2.845370 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): 3.013000 58.63000 ymin,ymax (A): 4.969000 61.27100 zmin,zma (A): 6.583000 53.94300 x,y,z range (A): 55.61700 56.30200 47.36000 scale (grids/A): 2.845370 object centre (A): 30.82150 33.12000 30.26300 number of atom coordinates read : 2642 total number of charged atoms : 2469 net assigned charge : 5.500015 assigned positive charge : 395.1147 centred at (gu) : 92.38601 89.75241 97.72086 assigned negative charge : -389.6153 centred at (gu) : 92.50709 89.58067 97.57502 start vw surface at 0.1200000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 180016 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26001 grid for indexing accessible points = 1.400000 m= 88186 mr = 127351 m= 30496 mr = 70185 m= 7014 mr = 23366 m= 1072 mr = 4854 m= 73 mr = 673 m= 1 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 1.030000 no. cavity mid-points inaccessible to solvent = 323 time to turn everything in is 1.680000 number of dielectric boundary points 80408 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.820000 number of grid points assigned charge 19751 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) : 1.896913 object centre at (A) : 30.82150 33.12000 30.26300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1386980 0.3430012 midg,1,midg; midg,igrid,midg 0.4062842 2.7396597E-03 1,midg,midg; igrid,midg,midg 8.1423812E-02 -0.1188196 gauss-seidel spectral radius is 0.9992643 estimated iterations to convergence 291 setup time was (sec) 2.020000 now iterating at: 14:10:05 rms-change max change #iterations 10.09427 319.4616 at 10iterations 5.982264 125.2729 at 20iterations 3.510032 72.96111 at 30iterations 2.047724 43.44031 at 40iterations 1.196108 22.95483 at 50iterations 0.6951981 15.24426 at 60iterations 0.4027331 9.638044 at 70iterations 0.2336583 4.771700 at 80iterations 0.1350936 2.544588 at 90iterations 7.8176685E-02 1.406123 at 100iterations 4.5160409E-02 0.8198633 at 110iterations 2.6066475E-02 0.4973831 at 120iterations 1.5013515E-02 0.2831211 at 130iterations 8.6752567E-03 0.1610699 at 140iterations 4.9816798E-03 9.3757153E-02 at 150iterations 2.8690069E-03 5.0616264E-02 at 160iterations 1.6544601E-03 3.1578064E-02 at 170iterations 9.5365173E-04 1.7438889E-02 at 180iterations finished qdiffx linear iterations at : 14:10:21 total time elapsed so far: 18.05000 # loops : 180 mean,max change (kT/e) : 9.5365173E-04 1.7438889E-02 energy calculations done at 18.06000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.23000 DelPhi exited at 14:10:21 18.232u 0.451s 0:19.00 98.3% 0+0k 0+0io 0pf+0w