Mon Oct 10 13:59:38 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 13:59:38 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2576 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: 0.6525286 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): -25.17700 29.38000 ymin,ymax (A): 11.15900 63.54100 zmin,zma (A): -9.345000 36.24600 x,y,z range (A): 54.55700 52.38200 45.59100 scale (grids/A): 0.6525286 object centre (A): 2.101501 37.35000 13.45050 number of atom coordinates read : 2576 total number of charged atoms : 2432 net assigned charge : 5.000012 assigned positive charge : 388.4979 centred at (gu) : 89.90304 90.22195 91.02921 assigned negative charge : -383.4987 centred at (gu) : 89.84945 90.25240 90.98882 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7194 nv = 96 ne = 84 npr = 52438 no. pairs analyzed = 52438 no. exposed pairs = 3010 no. arc points = 21541 no. surface atoms = 1028 nbur = 1548 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 380 mr = 3967 m= 3 mr = 59 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 42 time to turn everything in is 0.3100000 number of dielectric boundary points 3551 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2149 ## 178 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8654 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.1286183E-09 2.0797589E-08 midg,1,midg; midg,igrid,midg 1.4511580E-08 5.6173315E-09 1,midg,midg; igrid,midg,midg 1.6472896E-09 1.8505096E-08 gauss-seidel spectral radius is 0.9878259 estimated iterations to convergence 74 setup time was (sec) 0.5600000 now iterating at: 13:59:39 rms-change max change #iterations 0.1531893 20.92882 at 10iterations 1.6007286E-02 2.551054 at 20iterations 1.6727400E-03 0.2169151 at 30iterations 1.7481986E-04 2.6245117E-02 at 40iterations 1.7974111E-05 2.6435852E-03 at 50iterations finished qdiffx linear iterations at : 13:59:43 total time elapsed so far: 4.390000 # loops : 50 mean,max change (kT/e) : 1.7974111E-05 2.6435852E-03 energy calculations done at 4.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.560000 DelPhi exited at 13:59:44 4.561u 0.385s 0:05.38 91.8% 0+0k 0+0io 6pf+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 13:59:44 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2576 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: 1.957586 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): -25.17700 29.38000 ymin,ymax (A): 11.15900 63.54100 zmin,zma (A): -9.345000 36.24600 x,y,z range (A): 54.55700 52.38200 45.59100 scale (grids/A): 1.957586 object centre (A): 2.101501 37.35000 13.45050 number of atom coordinates read : 2576 total number of charged atoms : 2432 net assigned charge : 5.000012 assigned positive charge : 388.4979 centred at (gu) : 89.70853 90.66515 93.08694 assigned negative charge : -383.4987 centred at (gu) : 89.54819 90.75745 92.96655 start vw surface at 0.1100000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 78092 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21541 grid for indexing accessible points = 1.400000 m= 27559 mr = 54415 m= 4399 mr = 20382 m= 346 mr = 2849 m= 8 mr = 161 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 1675 time to turn everything in is 0.6200000 number of dielectric boundary points 32597 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 145 iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 19168 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) : 0.6525286 object centre at (A) : 2.101501 37.35000 13.45050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.0832154E-02 1.0536212E-02 midg,1,midg; midg,igrid,midg 2.9842131E-02 -1.5257299E-02 1,midg,midg; igrid,midg,midg 4.6650771E-02 2.4911582E-02 gauss-seidel spectral radius is 0.9986931 estimated iterations to convergence 219 setup time was (sec) 0.9300000 now iterating at: 13:59:45 rms-change max change #iterations 4.426958 180.1393 at 10iterations 2.099870 71.86560 at 20iterations 0.9994433 36.04565 at 30iterations 0.4741585 15.07487 at 40iterations 0.2262885 6.420055 at 50iterations 0.1074243 3.186998 at 60iterations 5.1251382E-02 1.705181 at 70iterations 2.4335383E-02 0.6987270 at 80iterations 1.1563107E-02 0.3606262 at 90iterations 5.5191126E-03 0.1765213 at 100iterations 2.6306375E-03 8.3854675E-02 at 110iterations 1.2505559E-03 4.1510105E-02 at 120iterations finished qdiffx linear iterations at : 13:59:55 total time elapsed so far: 11.28000 # loops : 120 mean,max change (kT/e) : 1.2505559E-03 4.1510105E-02 energy calculations done at 11.28000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.45000 DelPhi exited at 13:59:58 11.457u 0.437s 0:14.49 81.9% 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 13:59:58 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2576 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: 2.936378 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): -25.17700 29.38000 ymin,ymax (A): 11.15900 63.54100 zmin,zma (A): -9.345000 36.24600 x,y,z range (A): 54.55700 52.38200 45.59100 scale (grids/A): 2.936378 object centre (A): 2.101501 37.35000 13.45050 number of atom coordinates read : 2576 total number of charged atoms : 2432 net assigned charge : 5.000012 assigned positive charge : 388.4979 centred at (gu) : 89.56271 90.99763 94.63036 assigned negative charge : -383.4987 centred at (gu) : 89.32220 91.13612 94.44962 start vw surface at 0.1200000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 180718 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21541 grid for indexing accessible points = 1.400000 m= 89987 mr = 131540 m= 32047 mr = 74230 m= 8092 mr = 25765 m= 1371 mr = 6129 m= 104 mr = 1036 m= 1 mr = 62 m= 0 mr = 0 time to grow re-entrant surface = 1.000000 no. cavity mid-points inaccessible to solvent = 5778 time to turn everything in is 1.670000 number of dielectric boundary points 73558 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.810000 number of grid points assigned charge 19456 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) : 1.957586 object centre at (A) : 2.101501 37.35000 13.45050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1592043 0.1658626 midg,1,midg; midg,igrid,midg 0.3766351 -0.3121172 1,midg,midg; igrid,midg,midg 9.1799937E-02 0.2266288 gauss-seidel spectral radius is 0.9992719 estimated iterations to convergence 292 setup time was (sec) 2.010000 now iterating at: 14:00:01 rms-change max change #iterations 10.17260 343.2626 at 10iterations 5.901215 121.8760 at 20iterations 3.430336 71.70146 at 30iterations 1.983510 37.19199 at 40iterations 1.148463 20.91031 at 50iterations 0.6637852 12.42793 at 60iterations 0.3827189 7.257908 at 70iterations 0.2213912 3.768051 at 80iterations 0.1277529 2.291741 at 90iterations 7.3653705E-02 1.285515 at 100iterations 4.2488735E-02 0.7232132 at 110iterations 2.4528142E-02 0.4206309 at 120iterations 1.4113569E-02 0.2604408 at 130iterations 8.1544090E-03 0.1385887 at 140iterations 4.7040675E-03 7.9589844E-02 at 150iterations 2.7157818E-03 4.8269272E-02 at 160iterations 1.5667969E-03 2.8476715E-02 at 170iterations 9.0230303E-04 1.4984131E-02 at 180iterations finished qdiffx linear iterations at : 14:00:20 total time elapsed so far: 19.67000 # loops : 180 mean,max change (kT/e) : 9.0230303E-04 1.4984131E-02 energy calculations done at 19.67000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.84000 DelPhi exited at 14:00:21 19.844u 0.455s 0:22.26 91.1% 0+0k 0+0io 0pf+0w