Sun Oct 9 04:34:31 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 04:34:31 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 = 4660 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: 0.5068554 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): -12.16600 51.28600 ymin,ymax (A): -25.57400 38.85000 zmin,zma (A): 26.64300 96.88000 x,y,z range (A): 63.45200 64.42400 70.23700 scale (grids/A): 0.5068554 object centre (A): 19.56000 6.638000 61.76150 number of atom coordinates read : 4660 total number of charged atoms : 4511 net assigned charge : 8.500035 assigned positive charge : 680.6013 centred at (gu) : 89.02782 90.24631 90.51698 assigned negative charge : -672.1051 centred at (gu) : 88.92687 90.29916 90.68422 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 8015 nv = 96 ne = 84 npr = 89715 no. pairs analyzed = 89715 no. exposed pairs = 6593 no. arc points = 46360 no. surface atoms = 2190 nbur = 2470 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 = 1.680000 m= 334 mr = 3810 m= 2 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4700000 number of dielectric boundary points 4530 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4419 ## 618 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 10519 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.8892295E-10 -2.8602370E-10 midg,1,midg; midg,igrid,midg 2.0223344E-10 -4.1108462E-12 1,midg,midg; igrid,midg,midg -1.3877395E-10 2.4254593E-10 gauss-seidel spectral radius is 0.9801111 estimated iterations to convergence 59 setup time was (sec) 0.6800000 now iterating at: 04:34:32 rms-change max change #iterations 6.0119491E-02 8.892256 at 10iterations 5.0430573E-03 0.8399944 at 20iterations 1.7677635E-03 0.2993259 at 30iterations 8.0078514E-04 0.1356945 at 40iterations 3.6474975E-04 6.1624527E-02 at 50iterations finished qdiffx linear iterations at : 04:34:35 total time elapsed so far: 3.150000 # loops : 50 mean,max change (kT/e) : 3.6474975E-04 6.1624527E-02 energy calculations done at 3.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.300000 DelPhi exited at 04:34:35 3.307u 0.159s 0:03.76 91.7% 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 Sun Oct 9 2011 at 04:34:35 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 = 4660 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.520566 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): -12.16600 51.28600 ymin,ymax (A): -25.57400 38.85000 zmin,zma (A): 26.64300 96.88000 x,y,z range (A): 63.45200 64.42400 70.23700 scale (grids/A): 1.520566 object centre (A): 19.56000 6.638000 61.76150 number of atom coordinates read : 4660 total number of charged atoms : 4511 net assigned charge : 8.500035 assigned positive charge : 680.6013 centred at (gu) : 87.08204 90.73726 91.54926 assigned negative charge : -672.1051 centred at (gu) : 86.78033 90.89700 92.05219 start vw surface at 0.1900000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 89495 reading accessible surface arcs data from file ARCDAT no. of arc points read = 46360 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 27322 mr = 58571 m= 2625 mr = 17529 m= 70 mr = 1036 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6400000 number of dielectric boundary points 42377 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 572 ## 8 charges are in solution ## iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 33871 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) : 0.5068554 object centre at (A) : 19.56000 6.638000 61.76150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.4215773E-03 -1.0018714E-02 midg,1,midg; midg,igrid,midg 9.5056221E-03 4.5056413E-03 1,midg,midg; igrid,midg,midg -7.1594780E-03 -1.4205873E-03 gauss-seidel spectral radius is 0.9981045 estimated iterations to convergence 183 setup time was (sec) 0.9000000 now iterating at: 04:34:36 rms-change max change #iterations 3.612966 160.6200 at 10iterations 1.471128 50.31487 at 20iterations 0.6031851 19.83646 at 30iterations 0.2467596 8.288872 at 40iterations 0.1013793 3.661132 at 50iterations 4.1795831E-02 1.361645 at 60iterations 1.7519049E-02 0.5819149 at 70iterations 7.6889358E-03 0.2694321 at 80iterations 3.7837734E-03 0.1578722 at 90iterations 2.1926612E-03 8.3585739E-02 at 100iterations 1.4702204E-03 5.2818298E-02 at 110iterations 1.0609063E-03 3.7307739E-02 at 120iterations finished qdiffx linear iterations at : 04:34:43 total time elapsed so far: 7.310000 # loops : 120 mean,max change (kT/e) : 1.0609063E-03 3.7307739E-02 energy calculations done at 7.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.480000 DelPhi exited at 04:34:43 7.479u 0.210s 0:07.96 96.4% 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 Sun Oct 9 2011 at 04:34:43 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 = 4660 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.280849 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): -12.16600 51.28600 ymin,ymax (A): -25.57400 38.85000 zmin,zma (A): 26.64300 96.88000 x,y,z range (A): 63.45200 64.42400 70.23700 scale (grids/A): 2.280849 object centre (A): 19.56000 6.638000 61.76150 number of atom coordinates read : 4660 total number of charged atoms : 4511 net assigned charge : 8.500035 assigned positive charge : 680.6013 centred at (gu) : 85.62283 91.10567 92.32367 assigned negative charge : -672.1051 centred at (gu) : 85.17038 91.34524 93.07806 start vw surface at 0.1900000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 207583 reading accessible surface arcs data from file ARCDAT no. of arc points read = 46360 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 94186 mr = 144252 m= 26210 mr = 71454 m= 3772 mr = 18303 m= 158 mr = 2157 m= 5 mr = 29 m= 0 mr = 0 time to grow re-entrant surface = 0.9100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.530000 number of dielectric boundary points 95719 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 64 iepsmp to db, and charging done at 1.690000 number of grid points assigned charge 35964 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) : 1.520566 object centre at (A) : 19.56000 6.638000 61.76150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1124082 -0.3491240 midg,1,midg; midg,igrid,midg 0.1412782 5.3360041E-02 1,midg,midg; igrid,midg,midg -9.2966639E-02 -0.1772041 gauss-seidel spectral radius is 0.9991698 estimated iterations to convergence 274 setup time was (sec) 1.860000 now iterating at: 04:34:45 rms-change max change #iterations 9.995371 268.0662 at 10iterations 5.782173 146.8451 at 20iterations 3.289672 81.66016 at 30iterations 1.877593 47.03132 at 40iterations 1.061949 23.40683 at 50iterations 0.5989719 14.31171 at 60iterations 0.3371917 7.855473 at 70iterations 0.1889429 4.367295 at 80iterations 0.1056300 2.127609 at 90iterations 5.9174310E-02 1.153852 at 100iterations 3.3078723E-02 0.7185593 at 110iterations 1.8543286E-02 0.3759098 at 120iterations 1.0417260E-02 0.2136459 at 130iterations 5.9078461E-03 0.1122704 at 140iterations 3.4042147E-03 6.7424774E-02 at 150iterations 2.0288927E-03 4.2249680E-02 at 160iterations 1.2769436E-03 2.7732849E-02 at 170iterations 8.6509419E-04 1.9655228E-02 at 180iterations finished qdiffx linear iterations at : 04:34:56 total time elapsed so far: 12.99000 # loops : 180 mean,max change (kT/e) : 8.6509419E-04 1.9655228E-02 energy calculations done at 12.99000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.16000 DelPhi exited at 04:34:57 13.164u 0.204s 0:13.64 97.9% 0+0k 0+0io 0pf+0w