Sat Oct 8 11:39:48 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 11:39:48 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 = 3570 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5819466 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): 13.32100 74.49500 ymin,ymax (A): -1.450000 51.09300 zmin,zma (A): 22.40100 77.85800 x,y,z range (A): 61.17400 52.54300 55.45700 scale (grids/A): 0.5819466 object centre (A): 43.90800 24.82150 50.12950 number of atom coordinates read : 3570 total number of charged atoms : 3448 net assigned charge : -4.499970 assigned positive charge : 546.5427 centred at (gu) : 88.04256 91.11244 89.59159 assigned negative charge : -551.0442 centred at (gu) : 88.11449 90.98288 89.60348 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7933 nv = 96 ne = 84 npr = 72650 no. pairs analyzed = 72650 no. exposed pairs = 4080 no. arc points = 28527 no. surface atoms = 1380 nbur = 2190 mkacc time = 0.1500000 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 = 1.456000 m= 321 mr = 4584 m= 0 mr = 23 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 65 time to turn everything in is 0.3500000 number of dielectric boundary points 3647 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2804 ## 302 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 10101 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.6868324E-10 -1.3492391E-09 midg,1,midg; midg,igrid,midg -3.8136112E-09 3.3542626E-09 1,midg,midg; igrid,midg,midg 1.5242857E-09 -2.0586544E-09 gauss-seidel spectral radius is 0.9847996 estimated iterations to convergence 67 setup time was (sec) 0.5700000 now iterating at: 11:39:49 rms-change max change #iterations 0.1154884 17.10380 at 10iterations 9.3598841E-03 1.508995 at 20iterations 7.4271340E-04 0.1074753 at 30iterations 6.1325758E-05 7.9460144E-03 at 40iterations 5.3330964E-06 7.7819824E-04 at 50iterations finished qdiffx linear iterations at : 11:39:51 total time elapsed so far: 3.050000 # loops : 50 mean,max change (kT/e) : 5.3330964E-06 7.7819824E-04 energy calculations done at 3.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.230000 DelPhi exited at 11:39:52 3.229u 0.176s 0:03.78 89.6% 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 11:39:52 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3570 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: 1.745840 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): 13.32100 74.49500 ymin,ymax (A): -1.450000 51.09300 zmin,zma (A): 22.40100 77.85800 x,y,z range (A): 61.17400 52.54300 55.45700 scale (grids/A): 1.745840 object centre (A): 43.90800 24.82150 50.12950 number of atom coordinates read : 3570 total number of charged atoms : 3448 net assigned charge : -4.499970 assigned positive charge : 546.5427 centred at (gu) : 84.12637 93.33614 88.77351 assigned negative charge : -551.0442 centred at (gu) : 84.34288 92.94801 88.80979 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 87493 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28527 grid for indexing accessible points = 1.400000 m= 29621 mr = 62569 m= 3691 mr = 22282 m= 139 mr = 2256 m= 1 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 3663 time to turn everything in is 0.5500000 number of dielectric boundary points 33802 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 238 iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 26742 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) : 0.5819466 object centre at (A) : 43.90800 24.82150 50.12950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3478108E-02 -1.5090253E-02 midg,1,midg; midg,igrid,midg -1.7430261E-02 1.6157631E-02 1,midg,midg; igrid,midg,midg 2.3360900E-04 -2.7932657E-03 gauss-seidel spectral radius is 0.9984676 estimated iterations to convergence 203 setup time was (sec) 0.8100000 now iterating at: 11:39:54 rms-change max change #iterations 4.335088 167.1317 at 10iterations 1.944163 71.45193 at 20iterations 0.8728690 28.80337 at 30iterations 0.3899001 11.97975 at 40iterations 0.1747034 5.247328 at 50iterations 7.8473568E-02 2.437093 at 60iterations 3.5170615E-02 1.088351 at 70iterations 1.5735576E-02 0.4751472 at 80iterations 7.0505268E-03 0.2051868 at 90iterations 3.1731552E-03 9.2847824E-02 at 100iterations 1.4219134E-03 4.2855263E-02 at 110iterations 6.3774729E-04 1.8233061E-02 at 120iterations finished qdiffx linear iterations at : 11:40:04 total time elapsed so far: 7.080000 # loops : 120 mean,max change (kT/e) : 6.3774729E-04 1.8233061E-02 energy calculations done at 7.080000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.270000 DelPhi exited at 11:40:04 7.275u 0.171s 0:12.51 59.4% 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 11:40:04 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 = 3570 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.618760 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): 13.32100 74.49500 ymin,ymax (A): -1.450000 51.09300 zmin,zma (A): 22.40100 77.85800 x,y,z range (A): 61.17400 52.54300 55.45700 scale (grids/A): 2.618760 object centre (A): 43.90800 24.82150 50.12950 number of atom coordinates read : 3570 total number of charged atoms : 3448 net assigned charge : -4.499970 assigned positive charge : 546.5427 centred at (gu) : 81.18928 95.00387 88.16000 assigned negative charge : -551.0442 centred at (gu) : 81.51427 94.42186 88.21452 start vw surface at 0.1700000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 203036 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28527 grid for indexing accessible points = 1.400000 m= 99936 mr = 151735 m= 32238 mr = 82823 m= 6263 mr = 26227 m= 648 mr = 4654 m= 11 mr = 417 m= 0 mr = 4 time to grow re-entrant surface = 0.8200000 no. cavity mid-points inaccessible to solvent = 12677 time to turn everything in is 1.390000 number of dielectric boundary points 76272 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 1.520000 number of grid points assigned charge 27577 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) : 1.745840 object centre at (A) : 43.90800 24.82150 50.12950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1904979 -0.2191316 midg,1,midg; midg,igrid,midg -0.1972390 0.1361543 1,midg,midg; igrid,midg,midg -9.7880270E-03 5.4967102E-02 gauss-seidel spectral radius is 0.9992225 estimated iterations to convergence 283 setup time was (sec) 1.680000 now iterating at: 11:40:06 rms-change max change #iterations 10.50890 276.2259 at 10iterations 6.035903 136.5422 at 20iterations 3.448684 67.22089 at 30iterations 1.960625 36.89410 at 40iterations 1.116841 19.01875 at 50iterations 0.6344140 12.10783 at 60iterations 0.3594179 6.052227 at 70iterations 0.2040285 3.774483 at 80iterations 0.1156775 1.886330 at 90iterations 6.5523647E-02 1.232063 at 100iterations 3.7176542E-02 0.6561203 at 110iterations 2.1039836E-02 0.3743261 at 120iterations 1.1934678E-02 0.2062149 at 130iterations 6.7578736E-03 0.1159897 at 140iterations 3.8236245E-03 6.9109619E-02 at 150iterations 2.1698775E-03 3.5518646E-02 at 160iterations 1.2285445E-03 2.1255255E-02 at 170iterations 6.9470180E-04 1.1894226E-02 at 180iterations finished qdiffx linear iterations at : 11:40:22 total time elapsed so far: 11.36000 # loops : 180 mean,max change (kT/e) : 6.9470180E-04 1.1894226E-02 energy calculations done at 11.36000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.53000 DelPhi exited at 11:40:23 11.533u 0.171s 0:18.75 62.4% 0+0k 0+0io 0pf+0w