Sat Oct 8 18:24:19 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 Sat Oct 8 2011 at 18:24:19 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 = 3268 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: 0.5549753 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): -14.55900 44.68800 ymin,ymax (A): -71.59900 -7.452000 zmin,zma (A): -21.74100 25.75000 x,y,z range (A): 59.24700 64.14700 47.49100 scale (grids/A): 0.5549753 object centre (A): 15.06450 -39.52550 2.004499 number of atom coordinates read : 3268 total number of charged atoms : 3124 net assigned charge : -4.999983 assigned positive charge : 488.3718 centred at (gu) : 89.84418 90.60691 89.65030 assigned negative charge : -493.3730 centred at (gu) : 89.82222 90.60766 89.63446 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6714 nv = 96 ne = 84 npr = 65195 no. pairs analyzed = 65195 no. exposed pairs = 4142 no. arc points = 28424 no. surface atoms = 1403 nbur = 1865 mkacc time = 0.1700000 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 = 1.540000 m= 291 mr = 3661 m= 2 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 3337 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2870 ## 368 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 8616 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.5508443E-10 -2.5562222E-10 midg,1,midg; midg,igrid,midg -3.7419140E-10 -5.1628413E-10 1,midg,midg; igrid,midg,midg -6.9088019E-10 -2.0703073E-10 gauss-seidel spectral radius is 0.9832779 estimated iterations to convergence 64 setup time was (sec) 0.6200000 now iterating at: 18:24:20 rms-change max change #iterations 8.4535189E-02 12.25636 at 10iterations 5.8738086E-03 0.9807489 at 20iterations 4.4000419E-04 6.3880920E-02 at 30iterations 5.0790168E-05 9.8457336E-03 at 40iterations 1.1724913E-05 2.7446747E-03 at 50iterations finished qdiffx linear iterations at : 18:24:23 total time elapsed so far: 4.350000 # loops : 50 mean,max change (kT/e) : 1.1724913E-05 2.7446747E-03 energy calculations done at 4.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.530000 DelPhi exited at 18:24:24 4.531u 0.417s 0:05.25 94.0% 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 8 2011 at 18:24:24 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 = 3268 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: 1.664926 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): -14.55900 44.68800 ymin,ymax (A): -71.59900 -7.452000 zmin,zma (A): -21.74100 25.75000 x,y,z range (A): 59.24700 64.14700 47.49100 scale (grids/A): 1.664926 object centre (A): 15.06450 -39.52550 2.004499 number of atom coordinates read : 3268 total number of charged atoms : 3124 net assigned charge : -4.999983 assigned positive charge : 488.3718 centred at (gu) : 89.53193 91.81985 88.94985 assigned negative charge : -493.3730 centred at (gu) : 89.46636 91.82259 88.90291 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 74335 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28424 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 24476 mr = 51857 m= 2811 mr = 17271 m= 97 mr = 1421 m= 0 mr = 15 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6200000 number of dielectric boundary points 31155 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 295 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 24039 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) : 0.5549753 object centre at (A) : 15.06450 -39.52550 2.004499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.3662653E-03 -5.8113271E-03 midg,1,midg; midg,igrid,midg 7.9832235E-03 1.3416841E-02 1,midg,midg; igrid,midg,midg -2.2911111E-02 -2.3564857E-03 gauss-seidel spectral radius is 0.9982884 estimated iterations to convergence 192 setup time was (sec) 0.9300000 now iterating at: 18:24:25 rms-change max change #iterations 3.668406 173.4167 at 10iterations 1.558914 55.92130 at 20iterations 0.6695997 28.30291 at 30iterations 0.2867096 9.987962 at 40iterations 0.1223535 4.264633 at 50iterations 5.2428909E-02 1.927457 at 60iterations 2.2473937E-02 0.7696838 at 70iterations 9.6408678E-03 0.3433952 at 80iterations 4.1176947E-03 0.1450405 at 90iterations 1.7732681E-03 5.9324086E-02 at 100iterations 7.5901888E-04 2.5191784E-02 at 110iterations 3.3061646E-04 1.2046814E-02 at 120iterations finished qdiffx linear iterations at : 18:24:35 total time elapsed so far: 10.72000 # loops : 120 mean,max change (kT/e) : 3.3061646E-04 1.2046814E-02 energy calculations done at 10.72000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.88000 DelPhi exited at 18:24:36 10.883u 0.453s 0:11.60 97.6% 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 8 2011 at 18:24:36 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 = 3268 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.497389 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): -14.55900 44.68800 ymin,ymax (A): -71.59900 -7.452000 zmin,zma (A): -21.74100 25.75000 x,y,z range (A): 59.24700 64.14700 47.49100 scale (grids/A): 2.497389 object centre (A): 15.06450 -39.52550 2.004499 number of atom coordinates read : 3268 total number of charged atoms : 3124 net assigned charge : -4.999983 assigned positive charge : 488.3718 centred at (gu) : 89.29771 92.72964 88.42442 assigned negative charge : -493.3730 centred at (gu) : 89.19952 92.73387 88.35430 start vw surface at 0.1300000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 172547 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28424 grid for indexing accessible points = 1.400000 m= 83730 mr = 126367 m= 25088 mr = 67341 m= 4404 mr = 19127 m= 375 mr = 2957 m= 8 mr = 174 m= 0 mr = 0 time to grow re-entrant surface = 0.9300001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.500000 number of dielectric boundary points 70186 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 21 iepsmp to db, and charging done at 1.640000 number of grid points assigned charge 24969 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) : 1.664926 object centre at (A) : 15.06450 -39.52550 2.004499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.2352288E-02 -6.1760433E-02 midg,1,midg; midg,igrid,midg 0.3410681 0.4047191 1,midg,midg; igrid,midg,midg -0.2918951 -2.2578688E-02 gauss-seidel spectral radius is 0.9991769 estimated iterations to convergence 275 setup time was (sec) 1.830000 now iterating at: 18:24:38 rms-change max change #iterations 9.363278 280.2733 at 10iterations 5.316092 132.2813 at 20iterations 3.002493 64.31652 at 30iterations 1.699011 38.10983 at 40iterations 0.9535794 20.02005 at 50iterations 0.5351322 13.46247 at 60iterations 0.2996566 5.835146 at 70iterations 0.1671540 3.730363 at 80iterations 9.3596846E-02 1.874271 at 90iterations 5.2306246E-02 1.087414 at 100iterations 2.9197430E-02 0.6018224 at 110iterations 1.6343713E-02 0.3066330 at 120iterations 9.1007296E-03 0.1735363 at 130iterations 5.0694500E-03 0.1068730 at 140iterations 2.8376428E-03 5.7879448E-02 at 150iterations 1.5845416E-03 2.8773069E-02 at 160iterations 8.8623178E-04 1.6379833E-02 at 170iterations 4.9757527E-04 9.8114014E-03 at 180iterations finished qdiffx linear iterations at : 18:24:54 total time elapsed so far: 17.78000 # loops : 180 mean,max change (kT/e) : 4.9757527E-04 9.8114014E-03 energy calculations done at 17.78000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.94000 DelPhi exited at 18:24:54 17.942u 0.502s 0:18.72 98.5% 0+0k 0+0io 0pf+0w