Mon Oct 10 17:13:55 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 17:13:55 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: 308 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1847 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6988889 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): -26.92600 23.97000 ymin,ymax (A): -1.836000 37.92100 zmin,zma (A): 25.13800 76.07600 x,y,z range (A): 50.89600 39.75700 50.93800 scale (grids/A): 0.6988889 object centre (A): -1.478000 18.04250 50.60700 number of atom coordinates read : 1847 total number of charged atoms : 1717 net assigned charge : -7.999989 assigned positive charge : 264.6614 centred at (gu) : 88.06198 89.64040 91.35352 assigned negative charge : -272.6611 centred at (gu) : 88.10321 89.74096 91.42428 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 6228 nv = 96 ne = 84 npr = 38938 no. pairs analyzed = 38938 no. exposed pairs = 2424 no. arc points = 17524 no. surface atoms = 812 nbur = 1035 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 364 mr = 3274 m= 2 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 4 time to turn everything in is 0.2600000 number of dielectric boundary points 3278 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1502 ## 133 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 6855 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.3435655E-08 -1.0420067E-07 midg,1,midg; midg,igrid,midg -2.0707420E-08 -8.4597318E-08 1,midg,midg; igrid,midg,midg -5.7847686E-08 -4.7998984E-08 gauss-seidel spectral radius is 0.9893192 estimated iterations to convergence 79 setup time was (sec) 0.7400000 now iterating at: 17:13:56 rms-change max change #iterations 0.1880412 27.68049 at 10iterations 2.2369478E-02 3.036383 at 20iterations 2.6279124E-03 0.3690262 at 30iterations 3.1622068E-04 5.0880432E-02 at 40iterations 3.8063419E-05 5.7449341E-03 at 50iterations finished qdiffx linear iterations at : 17:14:03 total time elapsed so far: 7.260000 # loops : 50 mean,max change (kT/e) : 3.8063419E-05 5.7449341E-03 energy calculations done at 7.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.430000 DelPhi exited at 17:14:04 7.435u 0.679s 0:08.91 90.9% 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 17:14:04 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: 308 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1847 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.096667 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): -26.92600 23.97000 ymin,ymax (A): -1.836000 37.92100 zmin,zma (A): 25.13800 76.07600 x,y,z range (A): 50.89600 39.75700 50.93800 scale (grids/A): 2.096667 object centre (A): -1.478000 18.04250 50.60700 number of atom coordinates read : 1847 total number of charged atoms : 1717 net assigned charge : -7.999989 assigned positive charge : 264.6614 centred at (gu) : 84.18629 88.92131 94.06075 assigned negative charge : -272.6611 centred at (gu) : 84.30962 89.22293 94.27289 start vw surface at 0.1100000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 65662 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17524 grid for indexing accessible points = 1.400000 m= 23198 mr = 43825 m= 3735 mr = 16632 m= 251 mr = 2214 m= 3 mr = 93 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 406 time to turn everything in is 0.6200000 number of dielectric boundary points 30085 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 55 iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 13631 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) : 0.6988889 object centre at (A) : -1.478000 18.04250 50.60700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1047480 -9.4446510E-02 midg,1,midg; midg,igrid,midg 8.6930878E-03 -1.7531544E-02 1,midg,midg; igrid,midg,midg 1.2072039E-02 5.9040491E-03 gauss-seidel spectral radius is 0.9987981 estimated iterations to convergence 228 setup time was (sec) 1.030000 now iterating at: 17:14:05 rms-change max change #iterations 4.256373 183.0175 at 10iterations 2.073840 78.08739 at 20iterations 1.018365 34.13313 at 30iterations 0.4977848 16.88401 at 40iterations 0.2430933 8.138014 at 50iterations 0.1193517 3.960079 at 60iterations 5.8529835E-02 1.889874 at 70iterations 2.8762430E-02 0.9635696 at 80iterations 1.4083346E-02 0.4702148 at 90iterations 6.8931566E-03 0.2186394 at 100iterations 3.3836656E-03 0.1109114 at 110iterations 1.6662391E-03 5.0964355E-02 at 120iterations finished qdiffx linear iterations at : 17:14:21 total time elapsed so far: 16.20000 # loops : 120 mean,max change (kT/e) : 1.6662391E-03 5.0964355E-02 energy calculations done at 16.20000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.38000 DelPhi exited at 17:14:21 16.385u 0.693s 0:17.41 98.0% 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 17:14:21 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: 308 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1847 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 3.145000 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): -26.92600 23.97000 ymin,ymax (A): -1.836000 37.92100 zmin,zma (A): 25.13800 76.07600 x,y,z range (A): 50.89600 39.75700 50.93800 scale (grids/A): 3.145000 object centre (A): -1.478000 18.04250 50.60700 number of atom coordinates read : 1847 total number of charged atoms : 1717 net assigned charge : -7.999989 assigned positive charge : 264.6614 centred at (gu) : 81.27940 88.38218 96.09131 assigned negative charge : -272.6611 centred at (gu) : 81.46446 88.83449 96.40944 start vw surface at 0.1100000 fill in re-entrant regions at 0.7400000 boundary points on vw surface= 151439 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17524 grid for indexing accessible points = 1.400000 m= 74386 mr = 106093 m= 27151 mr = 59904 m= 6696 mr = 21368 m= 1067 mr = 4909 m= 88 mr = 699 m= 1 mr = 47 m= 0 mr = 0 time to grow re-entrant surface = 0.9300000 no. cavity mid-points inaccessible to solvent = 1309 time to turn everything in is 1.810000 number of dielectric boundary points 67808 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.010000 number of grid points assigned charge 13736 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) : 2.096667 object centre at (A) : -1.478000 18.04250 50.60700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.038472 -0.8654500 midg,1,midg; midg,igrid,midg 9.7402930E-02 -0.1123846 1,midg,midg; igrid,midg,midg 0.1420167 0.1790385 gauss-seidel spectral radius is 0.9992987 estimated iterations to convergence 298 setup time was (sec) 2.330000 now iterating at: 17:14:24 rms-change max change #iterations 9.464646 375.7488 at 10iterations 5.548213 130.2654 at 20iterations 3.260033 79.08907 at 30iterations 1.911334 38.94471 at 40iterations 1.119150 24.50196 at 50iterations 0.6531843 12.30513 at 60iterations 0.3825347 6.878769 at 70iterations 0.2228507 4.301819 at 80iterations 0.1300728 2.485549 at 90iterations 7.5755514E-02 1.437233 at 100iterations 4.4233747E-02 0.8508949 at 110iterations 2.5753668E-02 0.4970856 at 120iterations 1.5028547E-02 0.3100500 at 130iterations 8.7443599E-03 0.1612372 at 140iterations 5.0938022E-03 9.6599579E-02 at 150iterations 2.9660191E-03 5.1919937E-02 at 160iterations 1.7362772E-03 3.3748627E-02 at 170iterations 1.0114004E-03 1.8394470E-02 at 180iterations finished qdiffx linear iterations at : 17:14:51 total time elapsed so far: 28.94000 # loops : 180 mean,max change (kT/e) : 1.0114004E-03 1.8394470E-02 energy calculations done at 28.94000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 29.09000 DelPhi exited at 17:14:51 29.094u 0.818s 0:30.20 99.0% 0+0k 0+0io 0pf+0w