Sat Oct 15 10:52:27 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+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 15 2011 at 10:52:28 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: 258 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4055 !!! WARNING: HIT 440 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5981585 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): -25.52700 33.98900 ymin,ymax (A): 38.07100 96.13000 zmin,zma (A): 31.03700 89.04800 x,y,z range (A): 59.51600 58.05900 58.01100 scale (grids/A): 0.5981585 object centre (A): 4.231001 67.10050 60.04250 number of atom coordinates read : 4055 total number of charged atoms : 3911 net assigned charge : -3.485941 assigned positive charge : 604.1260 centred at (gu) : 90.95767 88.97558 89.20893 assigned negative charge : -607.6144 centred at (gu) : 90.81223 89.09657 89.34761 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 9519 nv = 96 ne = 84 npr = 84962 no. pairs analyzed = 84962 no. exposed pairs = 4620 no. arc points = 31521 no. surface atoms = 1559 nbur = 2496 mkacc time = 0.2400000 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= 435 mr = 5595 m= 0 mr = 39 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 218 time to turn everything in is 0.4900000 number of dielectric boundary points 4320 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3196 ## 312 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 12147 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.9151311E-09 -7.6780200E-09 midg,1,midg; midg,igrid,midg 6.1352483E-09 -6.5056347E-09 1,midg,midg; igrid,midg,midg -7.6936120E-09 7.6341404E-09 gauss-seidel spectral radius is 0.9856481 estimated iterations to convergence 68 setup time was (sec) 0.7700000 now iterating at: 10:52:29 rms-change max change #iterations 0.1333109 27.45707 at 10iterations 1.1785982E-02 1.490263 at 20iterations 1.3627295E-03 0.2021332 at 30iterations 3.1170738E-04 3.5128593E-02 at 40iterations 1.0669739E-04 1.3230801E-02 at 50iterations finished qdiffx linear iterations at : 10:52:39 total time elapsed so far: 4.070000 # loops : 50 mean,max change (kT/e) : 1.0669739E-04 1.3230801E-02 energy calculations done at 4.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.250000 DelPhi exited at 10:52:41 4.250u 0.285s 0:13.72 33.0% 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 10:52:42 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: 258 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4055 !!! WARNING: HIT 440 has a net charge of 0.5140 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: 1.794475 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): -25.52700 33.98900 ymin,ymax (A): 38.07100 96.13000 zmin,zma (A): 31.03700 89.04800 x,y,z range (A): 59.51600 58.05900 58.01100 scale (grids/A): 1.794475 object centre (A): 4.231001 67.10050 60.04250 number of atom coordinates read : 4055 total number of charged atoms : 3911 net assigned charge : -3.485941 assigned positive charge : 604.1260 centred at (gu) : 92.87194 86.92512 87.62547 assigned negative charge : -607.6144 centred at (gu) : 92.43619 87.28923 88.04247 start vw surface at 0.1900000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 105312 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31521 grid for indexing accessible points = 1.400000 m= 36849 mr = 76649 m= 5108 mr = 27497 m= 233 mr = 3221 m= 4 mr = 75 m= 0 mr = 0 time to grow re-entrant surface = 0.4600000 no. cavity mid-points inaccessible to solvent = 5882 time to turn everything in is 0.8900000 number of dielectric boundary points 40064 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 267 iepsmp to db, and charging done at 1.040000 number of grid points assigned charge 30532 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) : 0.5981585 object centre at (A) : 4.231001 67.10050 60.04250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.2717613E-02 -3.7471578E-02 midg,1,midg; midg,igrid,midg 2.7544413E-02 -1.9459352E-02 1,midg,midg; igrid,midg,midg -1.4935031E-02 5.5783954E-02 gauss-seidel spectral radius is 0.9985986 estimated iterations to convergence 212 setup time was (sec) 1.230000 now iterating at: 10:52:47 rms-change max change #iterations 4.878578 191.7437 at 10iterations 2.255094 66.09305 at 20iterations 1.045249 31.80186 at 30iterations 0.4857211 12.96534 at 40iterations 0.2258250 6.455772 at 50iterations 0.1050861 3.042477 at 60iterations 4.8732884E-02 1.315723 at 70iterations 2.2742473E-02 0.6030998 at 80iterations 1.0606016E-02 0.2815270 at 90iterations 4.9680332E-03 0.1321030 at 100iterations 2.3366876E-03 6.0964108E-02 at 110iterations 1.1204832E-03 3.2713175E-02 at 120iterations finished qdiffx linear iterations at : 10:53:10 total time elapsed so far: 10.08000 # loops : 120 mean,max change (kT/e) : 1.1204832E-03 3.2713175E-02 energy calculations done at 10.08000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.26000 DelPhi exited at 10:53:11 10.267u 0.330s 0:29.18 36.2% 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 10:53:11 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: 258 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4055 !!! WARNING: HIT 440 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.691713 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): -25.52700 33.98900 ymin,ymax (A): 38.07100 96.13000 zmin,zma (A): 31.03700 89.04800 x,y,z range (A): 59.51600 58.05900 58.01100 scale (grids/A): 2.691713 object centre (A): 4.231001 67.10050 60.04250 number of atom coordinates read : 4055 total number of charged atoms : 3911 net assigned charge : -3.485941 assigned positive charge : 604.1260 centred at (gu) : 94.30766 85.38736 86.43779 assigned negative charge : -607.6144 centred at (gu) : 93.65411 85.93376 87.06367 start vw surface at 0.2100000 fill in re-entrant regions at 0.7700000 boundary points on vw surface= 243834 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31521 grid for indexing accessible points = 1.400000 m= 123330 mr = 185229 m= 41283 mr = 102205 m= 9072 mr = 33259 m= 1067 mr = 6954 m= 48 mr = 650 m= 0 mr = 23 time to grow re-entrant surface = 1.430000 no. cavity mid-points inaccessible to solvent = 20359 time to turn everything in is 2.350000 number of dielectric boundary points 90314 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 2.510000 number of grid points assigned charge 31283 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) : 1.794475 object centre at (A) : 4.231001 67.10050 60.04250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.7018564 -0.4179564 midg,1,midg; midg,igrid,midg 0.3908600 -0.3391971 1,midg,midg; igrid,midg,midg -0.2455324 0.5824715 gauss-seidel spectral radius is 0.9992712 estimated iterations to convergence 292 setup time was (sec) 2.690000 now iterating at: 10:53:20 rms-change max change #iterations 11.72995 420.7227 at 10iterations 6.914136 165.5039 at 20iterations 4.052511 78.50301 at 30iterations 2.364586 42.38021 at 40iterations 1.379431 23.47163 at 50iterations 0.8006319 13.74898 at 60iterations 0.4663916 7.727909 at 70iterations 0.2699770 4.296487 at 80iterations 0.1564856 2.541202 at 90iterations 9.0611249E-02 1.591866 at 100iterations 5.2520081E-02 0.8108878 at 110iterations 3.0422522E-02 0.4915590 at 120iterations 1.7636772E-02 0.2927403 at 130iterations 1.0236655E-02 0.1550975 at 140iterations 5.9731123E-03 9.7130775E-02 at 150iterations 3.5125092E-03 5.6579590E-02 at 160iterations 2.0896089E-03 3.3267975E-02 at 170iterations 1.2704056E-03 2.2735596E-02 at 180iterations finished qdiffx linear iterations at : 10:53:57 total time elapsed so far: 17.69000 # loops : 180 mean,max change (kT/e) : 1.2704056E-03 2.2735596E-02 energy calculations done at 17.69000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.87000 DelPhi exited at 10:53:59 17.874u 0.373s 0:48.23 37.8% 0+0k 0+0io 0pf+0w