Mon Oct 10 17:03:52 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 17:03:52 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4692 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.5145550 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): -17.87500 36.03300 ymin,ymax (A): -30.58000 33.92900 zmin,zma (A): -3.917000 65.26900 x,y,z range (A): 53.90800 64.50900 69.18600 scale (grids/A): 0.5145550 object centre (A): 9.079000 1.674500 30.67600 number of atom coordinates read : 4692 total number of charged atoms : 4447 net assigned charge : 7.300035 assigned positive charge : 703.7556 centred at (gu) : 90.45523 90.28512 88.19989 assigned negative charge : -696.4600 centred at (gu) : 90.35657 90.35009 88.17200 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 7782 nv = 96 ne = 84 npr = 95187 no. pairs analyzed = 95187 no. exposed pairs = 5986 no. arc points = 41365 no. surface atoms = 2006 nbur = 2686 mkacc time = 0.2300000 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 = 1.652000 m= 279 mr = 3988 m= 0 mr = 3 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4800000 number of dielectric boundary points 4070 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3952 ## 585 charges are in solution ## iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 10380 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.1425760E-11 1.3037477E-10 midg,1,midg; midg,igrid,midg 2.9319530E-10 -7.7426676E-11 1,midg,midg; igrid,midg,midg -1.5357303E-10 4.6669146E-10 gauss-seidel spectral radius is 0.9806772 estimated iterations to convergence 59 setup time was (sec) 0.7300000 now iterating at: 17:03:53 rms-change max change #iterations 6.9629394E-02 9.942349 at 10iterations 4.0697227E-03 0.6146450 at 20iterations 3.6598387E-04 5.3962708E-02 at 30iterations 1.1236459E-04 1.7379761E-02 at 40iterations 4.5682264E-05 7.0900917E-03 at 50iterations finished qdiffx linear iterations at : 17:03:56 total time elapsed so far: 3.640000 # loops : 50 mean,max change (kT/e) : 4.5682264E-05 7.0900917E-03 energy calculations done at 3.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.830000 DelPhi exited at 17:03:57 3.835u 0.187s 0:04.47 89.7% 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 17:03:57 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4692 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.543665 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): -17.87500 36.03300 ymin,ymax (A): -30.58000 33.92900 zmin,zma (A): -3.917000 65.26900 x,y,z range (A): 53.90800 64.50900 69.18600 scale (grids/A): 1.543665 object centre (A): 9.079000 1.674500 30.67600 number of atom coordinates read : 4692 total number of charged atoms : 4447 net assigned charge : 7.300035 assigned positive charge : 703.7556 centred at (gu) : 91.36414 90.85394 84.59842 assigned negative charge : -696.4600 centred at (gu) : 91.06931 91.05001 84.51565 start vw surface at 0.2200000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 87679 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41365 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 25199 mr = 59660 m= 2288 mr = 16697 m= 48 mr = 969 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7100000 number of dielectric boundary points 37888 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 528 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.8700000 number of grid points assigned charge 33474 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) : 0.5145550 object centre at (A) : 9.079000 1.674500 30.67600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.6441817E-03 1.9232130E-02 midg,1,midg; midg,igrid,midg 9.9150008E-03 -1.0906432E-02 1,midg,midg; igrid,midg,midg -1.0635823E-03 1.0993238E-02 gauss-seidel spectral radius is 0.9981371 estimated iterations to convergence 184 setup time was (sec) 1.040000 now iterating at: 17:03:58 rms-change max change #iterations 3.830948 149.7479 at 10iterations 1.580015 53.94389 at 20iterations 0.6513872 22.33739 at 30iterations 0.2687073 8.812321 at 40iterations 0.1110151 3.637108 at 50iterations 4.6026967E-02 1.492508 at 60iterations 1.8947680E-02 0.6042290 at 70iterations 7.8289788E-03 0.2518826 at 80iterations 3.2455530E-03 0.1034584 at 90iterations 1.3435766E-03 4.0089607E-02 at 100iterations 5.5678765E-04 1.8751144E-02 at 110iterations 2.3012841E-04 7.5912476E-03 at 120iterations finished qdiffx linear iterations at : 17:04:05 total time elapsed so far: 8.600000 # loops : 120 mean,max change (kT/e) : 2.3012841E-04 7.5912476E-03 energy calculations done at 8.600000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.780000 DelPhi exited at 17:04:06 8.780u 0.212s 0:09.77 92.0% 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 Mon Oct 10 2011 at 17:04:07 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4692 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 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: 2.315497 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): -17.87500 36.03300 ymin,ymax (A): -30.58000 33.92900 zmin,zma (A): -3.917000 65.26900 x,y,z range (A): 53.90800 64.50900 69.18600 scale (grids/A): 2.315497 object centre (A): 9.079000 1.674500 30.67600 number of atom coordinates read : 4692 total number of charged atoms : 4447 net assigned charge : 7.300035 assigned positive charge : 703.7556 centred at (gu) : 92.04585 91.28055 81.89726 assigned negative charge : -696.4600 centred at (gu) : 91.60397 91.57495 81.77341 start vw surface at 0.2300000 fill in re-entrant regions at 0.5700000 boundary points on vw surface= 204254 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41365 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 90183 mr = 146611 m= 22882 mr = 70099 m= 3314 mr = 16331 m= 191 mr = 2036 m= 1 mr = 77 m= 0 mr = 0 time to grow re-entrant surface = 0.9400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.640000 number of dielectric boundary points 85671 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 72 iepsmp to db, and charging done at 1.800000 number of grid points assigned charge 35494 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) : 1.543665 object centre at (A) : 9.079000 1.674500 30.67600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1505898 0.4569376 midg,1,midg; midg,igrid,midg 0.1021811 -0.2778107 1,midg,midg; igrid,midg,midg -1.1714602E-02 0.1632053 gauss-seidel spectral radius is 0.9991680 estimated iterations to convergence 274 setup time was (sec) 1.990000 now iterating at: 17:04:09 rms-change max change #iterations 10.25057 325.7188 at 10iterations 5.874199 128.9112 at 20iterations 3.344646 67.34586 at 30iterations 1.893848 46.91016 at 40iterations 1.070459 23.84109 at 50iterations 0.6013619 12.30726 at 60iterations 0.3379089 7.471098 at 70iterations 0.1893916 4.008511 at 80iterations 0.1058000 2.116522 at 90iterations 5.9249416E-02 1.188693 at 100iterations 3.3048660E-02 0.6314678 at 110iterations 1.8453363E-02 0.3872857 at 120iterations 1.0283496E-02 0.1925297 at 130iterations 5.7407990E-03 0.1115379 at 140iterations 3.1961896E-03 6.3205957E-02 at 150iterations 1.7808586E-03 3.4450531E-02 at 160iterations 9.9357835E-04 1.9104004E-02 at 170iterations 5.5640965E-04 1.0608673E-02 at 180iterations finished qdiffx linear iterations at : 17:04:21 total time elapsed so far: 14.43000 # loops : 180 mean,max change (kT/e) : 5.5640965E-04 1.0608673E-02 energy calculations done at 14.43000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.64000 DelPhi exited at 17:04:22 14.643u 0.326s 0:15.69 95.3% 0+0k 0+0io 0pf+0w