Mon Oct 10 17:01:32 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 Mon Oct 10 2011 at 17:01:32 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2803 !!! WARNING: HIT 107 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5752420 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): -30.84000 31.04700 ymin,ymax (A): -22.05200 24.79300 zmin,zma (A): -7.364000 38.42300 x,y,z range (A): 61.88700 46.84500 45.78700 scale (grids/A): 0.5752420 object centre (A): 0.1034994 1.370500 15.52950 number of atom coordinates read : 2803 total number of charged atoms : 2664 net assigned charge : -2.985964 assigned positive charge : 423.0741 centred at (gu) : 90.48578 90.36037 89.73318 assigned negative charge : -426.0613 centred at (gu) : 90.58331 90.21844 89.69199 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6059 nv = 96 ne = 84 npr = 56597 no. pairs analyzed = 56597 no. exposed pairs = 3696 no. arc points = 25569 no. surface atoms = 1242 nbur = 1561 mkacc time = 0.1200000 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 = 1.512000 m= 243 mr = 3063 m= 0 mr = 15 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 19 time to turn everything in is 0.2900000 number of dielectric boundary points 3224 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2615 ## 287 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 7757 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.3772812E-09 1.7679155E-10 midg,1,midg; midg,igrid,midg -2.8888891E-09 2.1449313E-09 1,midg,midg; igrid,midg,midg 1.0544579E-09 -2.6098734E-09 gauss-seidel spectral radius is 0.9843916 estimated iterations to convergence 66 setup time was (sec) 0.5000000 now iterating at: 17:01:33 rms-change max change #iterations 9.1885224E-02 17.12477 at 10iterations 6.9938637E-03 1.065332 at 20iterations 5.2818464E-04 7.9885483E-02 at 30iterations 4.1052277E-05 6.3896179E-03 at 40iterations 3.1574168E-06 5.0735474E-04 at 50iterations finished qdiffx linear iterations at : 17:01:35 total time elapsed so far: 3.060000 # loops : 50 mean,max change (kT/e) : 3.1574168E-06 5.0735474E-04 energy calculations done at 3.060000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.230000 DelPhi exited at 17:01:38 3.233u 0.169s 0:05.91 57.3% 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 17:01:38 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2803 !!! WARNING: HIT 107 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= 0.1400000 grid size : 179 scale,in grids/A, set to be: 1.725726 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): -30.84000 31.04700 ymin,ymax (A): -22.05200 24.79300 zmin,zma (A): -7.364000 38.42300 x,y,z range (A): 61.88700 46.84500 45.78700 scale (grids/A): 1.725726 object centre (A): 0.1034994 1.370500 15.52950 number of atom coordinates read : 2803 total number of charged atoms : 2664 net assigned charge : -2.985964 assigned positive charge : 423.0741 centred at (gu) : 91.45667 91.08047 89.19904 assigned negative charge : -426.0613 centred at (gu) : 91.74967 90.65501 89.07575 start vw surface at 0.2300000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 66550 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25569 grid for indexing accessible points = 1.400000 m= 20334 mr = 44525 m= 2188 mr = 13801 m= 61 mr = 1043 m= 1 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 888 time to turn everything in is 0.5500000 number of dielectric boundary points 29763 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 240 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 20668 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) : 0.5752420 object centre at (A) : 0.1034994 1.370500 15.52950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.8258295E-03 -4.0999912E-03 midg,1,midg; midg,igrid,midg -1.6640497E-02 1.3561803E-02 1,midg,midg; igrid,midg,midg 4.2184726E-03 -8.8948216E-03 gauss-seidel spectral radius is 0.9983629 estimated iterations to convergence 196 setup time was (sec) 0.8200000 now iterating at: 17:01:39 rms-change max change #iterations 3.676354 174.2520 at 10iterations 1.594447 67.96469 at 20iterations 0.6914585 22.79162 at 30iterations 0.3013991 11.31771 at 40iterations 0.1309080 4.917866 at 50iterations 5.6968648E-02 1.962273 at 60iterations 2.4881037E-02 0.8501668 at 70iterations 1.0812606E-02 0.3964205 at 80iterations 4.7231251E-03 0.1586113 at 90iterations 2.0496191E-03 6.9523811E-02 at 100iterations 8.9459069E-04 3.1772614E-02 at 110iterations 3.9002098E-04 1.3456345E-02 at 120iterations finished qdiffx linear iterations at : 17:01:45 total time elapsed so far: 7.040000 # loops : 120 mean,max change (kT/e) : 3.9002098E-04 1.3456345E-02 energy calculations done at 7.040000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.210000 DelPhi exited at 17:01:46 7.214u 0.197s 0:07.86 94.1% 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 17:01:46 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2803 !!! WARNING: HIT 107 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.588589 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): -30.84000 31.04700 ymin,ymax (A): -22.05200 24.79300 zmin,zma (A): -7.364000 38.42300 x,y,z range (A): 61.88700 46.84500 45.78700 scale (grids/A): 2.588589 object centre (A): 0.1034994 1.370500 15.52950 number of atom coordinates read : 2803 total number of charged atoms : 2664 net assigned charge : -2.985964 assigned positive charge : 423.0741 centred at (gu) : 92.18465 91.62032 88.79843 assigned negative charge : -426.0613 centred at (gu) : 92.62443 90.98242 88.61340 start vw surface at 0.2000000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 154861 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25569 grid for indexing accessible points = 1.400000 m= 69889 mr = 109495 m= 20393 mr = 54496 m= 3284 mr = 15185 m= 217 mr = 2111 m= 8 mr = 91 m= 0 mr = 0 time to grow re-entrant surface = 0.6200000 no. cavity mid-points inaccessible to solvent = 3205 time to turn everything in is 1.150000 number of dielectric boundary points 67274 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 1.270000 number of grid points assigned charge 21306 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) : 1.725726 object centre at (A) : 0.1034994 1.370500 15.52950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.6502639E-02 -5.4606996E-02 midg,1,midg; midg,igrid,midg -0.1747131 0.2120778 1,midg,midg; igrid,midg,midg 0.3863552 -8.9204935E-03 gauss-seidel spectral radius is 0.9991908 estimated iterations to convergence 278 setup time was (sec) 1.420000 now iterating at: 17:01:48 rms-change max change #iterations 9.178818 310.1661 at 10iterations 5.213603 156.3130 at 20iterations 2.959276 77.90010 at 30iterations 1.670033 44.82012 at 40iterations 0.9407901 24.62024 at 50iterations 0.5290989 12.72825 at 60iterations 0.2968116 6.010536 at 70iterations 0.1661913 3.396412 at 80iterations 9.3247488E-02 1.982050 at 90iterations 5.2388139E-02 1.052841 at 100iterations 2.9281083E-02 0.6334381 at 110iterations 1.6396750E-02 0.3332329 at 120iterations 9.1815814E-03 0.1839468 at 130iterations 5.1365891E-03 0.1024565 at 140iterations 2.8731506E-03 5.8910370E-02 at 150iterations 1.6095397E-03 3.6878586E-02 at 160iterations 8.9868472E-04 1.8251419E-02 at 170iterations 5.0306629E-04 9.7827911E-03 at 180iterations finished qdiffx linear iterations at : 17:01:57 total time elapsed so far: 10.93000 # loops : 180 mean,max change (kT/e) : 5.0306629E-04 9.7827911E-03 energy calculations done at 10.93000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.10000 DelPhi exited at 17:01:58 11.104u 0.205s 0:12.34 91.5% 0+0k 0+0io 0pf+0w