Sun Oct 9 07:46:13 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 Sun Oct 9 2011 at 07:46:13 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 = 2570 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: 0.5480717 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): -3.797000 42.16200 ymin,ymax (A): 35.71700 88.87400 zmin,zma (A): -3.168000 61.78700 x,y,z range (A): 45.95900 53.15700 64.95500 scale (grids/A): 0.5480717 object centre (A): 19.18250 62.29550 29.30950 number of atom coordinates read : 2570 total number of charged atoms : 2425 net assigned charge : -8.499981 assigned positive charge : 383.8618 centred at (gu) : 90.47610 88.89266 89.83656 assigned negative charge : -392.3623 centred at (gu) : 90.62193 88.60128 89.75028 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5092 nv = 96 ne = 84 npr = 51497 no. pairs analyzed = 51497 no. exposed pairs = 3541 no. arc points = 25407 no. surface atoms = 1194 nbur = 1376 mkacc time = 8.9999996E-02 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 = 1.568000 m= 216 mr = 2393 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 8.9999996E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 2906 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2546 ## 317 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 6530 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1370872E-09 -1.7684642E-12 midg,1,midg; midg,igrid,midg -3.2365661E-09 9.3350183E-10 1,midg,midg; igrid,midg,midg 3.2139985E-10 -1.6652795E-09 gauss-seidel spectral radius is 0.9828105 estimated iterations to convergence 63 setup time was (sec) 0.3800000 now iterating at: 07:46:14 rms-change max change #iterations 6.7891285E-02 12.63760 at 10iterations 4.4234809E-03 0.8037663 at 20iterations 2.8852897E-04 5.3464890E-02 at 30iterations 1.9650857E-05 3.6687851E-03 at 40iterations 1.3828048E-06 2.2983551E-04 at 50iterations finished qdiffx linear iterations at : 07:46:17 total time elapsed so far: 3.510000 # loops : 50 mean,max change (kT/e) : 1.3828048E-06 2.2983551E-04 energy calculations done at 3.510000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.640000 DelPhi exited at 07:46:18 3.648u 0.193s 0:04.30 89.0% 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 Sun Oct 9 2011 at 07:46:18 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 = 2570 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.644215 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): -3.797000 42.16200 ymin,ymax (A): 35.71700 88.87400 zmin,zma (A): -3.168000 61.78700 x,y,z range (A): 45.95900 53.15700 64.95500 scale (grids/A): 1.644215 object centre (A): 19.18250 62.29550 29.30950 number of atom coordinates read : 2570 total number of charged atoms : 2425 net assigned charge : -8.499981 assigned positive charge : 383.8618 centred at (gu) : 91.42747 86.67739 89.50922 assigned negative charge : -392.3623 centred at (gu) : 91.86539 85.80357 89.25042 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 55740 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25407 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 16748 mr = 35541 m= 1635 mr = 11154 m= 53 mr = 739 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 26742 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 282 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 18574 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) : 0.5480717 object centre at (A) : 19.18250 62.29550 29.30950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.3794038E-02 8.3994232E-03 midg,1,midg; midg,igrid,midg -2.3983305E-02 3.8508985E-03 1,midg,midg; igrid,midg,midg -2.9834933E-03 -9.9865766E-03 gauss-seidel spectral radius is 0.9981678 estimated iterations to convergence 186 setup time was (sec) 0.5200000 now iterating at: 07:46:19 rms-change max change #iterations 3.116483 170.1766 at 10iterations 1.291808 58.63279 at 20iterations 0.5327146 20.50209 at 30iterations 0.2209981 8.654392 at 40iterations 9.1340892E-02 3.590316 at 50iterations 3.8069148E-02 1.454290 at 60iterations 1.5746066E-02 0.5816579 at 70iterations 6.5329005E-03 0.2418890 at 80iterations 2.7039289E-03 0.1123648 at 90iterations 1.1265636E-03 4.8958778E-02 at 100iterations 4.6718711E-04 1.7663956E-02 at 110iterations 1.9417708E-04 7.7948570E-03 at 120iterations finished qdiffx linear iterations at : 07:46:26 total time elapsed so far: 7.450000 # loops : 120 mean,max change (kT/e) : 1.9417708E-04 7.7948570E-03 energy calculations done at 7.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.580000 DelPhi exited at 07:46:26 7.583u 0.239s 0:08.23 94.8% 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 Sun Oct 9 2011 at 07:46:26 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 = 2570 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: 2.466323 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): -3.797000 42.16200 ymin,ymax (A): 35.71700 88.87400 zmin,zma (A): -3.168000 61.78700 x,y,z range (A): 45.95900 53.15700 64.95500 scale (grids/A): 2.466323 object centre (A): 19.18250 62.29550 29.30950 number of atom coordinates read : 2570 total number of charged atoms : 2425 net assigned charge : -8.499981 assigned positive charge : 383.8618 centred at (gu) : 92.14104 85.01591 89.26355 assigned negative charge : -392.3623 centred at (gu) : 92.79804 83.70528 88.87557 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 129301 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25407 grid for indexing accessible points = 1.400000 m= 57928 mr = 87459 m= 15966 mr = 44855 m= 2408 mr = 11532 m= 148 mr = 1462 m= 2 mr = 61 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7000000 number of dielectric boundary points 60385 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 27 iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 19377 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) : 1.644215 object centre at (A) : 19.18250 62.29550 29.30950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.8809984 8.6944245E-02 midg,1,midg; midg,igrid,midg -0.3050766 7.2761230E-02 1,midg,midg; igrid,midg,midg -4.8809096E-02 -0.1369645 gauss-seidel spectral radius is 0.9991263 estimated iterations to convergence 267 setup time was (sec) 0.9200000 now iterating at: 07:46:27 rms-change max change #iterations 8.099103 327.5177 at 10iterations 4.507000 147.4525 at 20iterations 2.518005 63.55542 at 30iterations 1.392718 34.24201 at 40iterations 0.7719983 21.20961 at 50iterations 0.4251318 10.69772 at 60iterations 0.2348312 5.741318 at 70iterations 0.1289846 2.959039 at 80iterations 7.0827946E-02 1.539597 at 90iterations 3.8965095E-02 0.9137764 at 100iterations 2.1328339E-02 0.5091782 at 110iterations 1.1693853E-02 0.2819939 at 120iterations 6.4000152E-03 0.1601710 at 130iterations 3.5117015E-03 8.1122398E-02 at 140iterations 1.9197043E-03 4.1238785E-02 at 150iterations 1.0538748E-03 2.2742271E-02 at 160iterations 5.7411118E-04 1.3043165E-02 at 170iterations 3.1408976E-04 6.7422390E-03 at 180iterations finished qdiffx linear iterations at : 07:46:38 total time elapsed so far: 11.91000 # loops : 180 mean,max change (kT/e) : 3.1408976E-04 6.7422390E-03 energy calculations done at 11.91000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.05000 DelPhi exited at 07:46:39 12.050u 0.259s 0:12.63 97.3% 0+0k 0+0io 0pf+0w