Mon Oct 10 17:15:59 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 17:15:59 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 = 2711 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5623124 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): -26.35200 32.39900 ymin,ymax (A): -28.10700 29.67500 zmin,zma (A): 25.69900 89.00900 x,y,z range (A): 58.75100 57.78200 63.31001 scale (grids/A): 0.5623124 object centre (A): 3.023500 0.7839994 57.35400 number of atom coordinates read : 2711 total number of charged atoms : 2575 net assigned charge : 12.50002 assigned positive charge : 401.2225 centred at (gu) : 90.29987 90.96980 90.76357 assigned negative charge : -388.7234 centred at (gu) : 90.25330 91.07651 90.60921 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 5768 nv = 96 ne = 84 npr = 52164 no. pairs analyzed = 52164 no. exposed pairs = 3704 no. arc points = 26245 no. surface atoms = 1240 nbur = 1471 mkacc time = 0.1400000 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= 270 mr = 2828 m= 0 mr = 12 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 3198 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2659 ## 348 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 7350 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.6080390E-10 3.6489458E-09 midg,1,midg; midg,igrid,midg 2.0275761E-09 3.7223974E-10 1,midg,midg; igrid,midg,midg 8.9078467E-10 2.0739697E-09 gauss-seidel spectral radius is 0.9836746 estimated iterations to convergence 64 setup time was (sec) 0.6300000 now iterating at: 17:16:00 rms-change max change #iterations 7.7582702E-02 12.08034 at 10iterations 5.6827683E-03 0.8909101 at 20iterations 4.0447849E-04 6.1501503E-02 at 30iterations 2.8419181E-05 4.6672821E-03 at 40iterations 2.1115391E-06 3.8528442E-04 at 50iterations finished qdiffx linear iterations at : 17:16:04 total time elapsed so far: 4.430000 # loops : 50 mean,max change (kT/e) : 2.1115391E-06 3.8528442E-04 energy calculations done at 4.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.590000 DelPhi exited at 17:16:05 4.598u 0.410s 0:05.37 93.1% 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 17:16:05 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 = 2711 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.686937 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): -26.35200 32.39900 ymin,ymax (A): -28.10700 29.67500 zmin,zma (A): 25.69900 89.00900 x,y,z range (A): 58.75100 57.78200 63.31001 scale (grids/A): 1.686937 object centre (A): 3.023500 0.7839994 57.35400 number of atom coordinates read : 2711 total number of charged atoms : 2575 net assigned charge : 12.50002 assigned positive charge : 401.2225 centred at (gu) : 90.89906 92.90874 92.29021 assigned negative charge : -388.7234 centred at (gu) : 90.75972 93.22923 91.82747 start vw surface at 0.1200000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 63366 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26245 grid for indexing accessible points = 1.400000 m= 19124 mr = 41544 m= 2190 mr = 12762 m= 85 mr = 1027 m= 0 mr = 15 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 130 time to turn everything in is 0.5800000 number of dielectric boundary points 29417 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 309 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 19865 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) : 0.5623124 object centre at (A) : 3.023500 0.7839994 57.35400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.2303136E-02 2.0471053E-02 midg,1,midg; midg,igrid,midg 2.0321827E-02 1.6604908E-02 1,midg,midg; igrid,midg,midg 4.0071006E-03 1.2580816E-02 gauss-seidel spectral radius is 0.9982865 estimated iterations to convergence 192 setup time was (sec) 0.8800000 now iterating at: 17:16:06 rms-change max change #iterations 3.303886 151.4917 at 10iterations 1.405042 69.92905 at 20iterations 0.5955743 21.63198 at 30iterations 0.2542825 10.42326 at 40iterations 0.1083774 4.006056 at 50iterations 4.6231531E-02 1.655043 at 60iterations 1.9752108E-02 0.7123685 at 70iterations 8.4428219E-03 0.2943211 at 80iterations 3.5948053E-03 0.1462831 at 90iterations 1.5374348E-03 5.4338455E-02 at 100iterations 6.5526838E-04 2.4166107E-02 at 110iterations 2.8003551E-04 9.3479156E-03 at 120iterations finished qdiffx linear iterations at : 17:16:16 total time elapsed so far: 10.78000 # loops : 120 mean,max change (kT/e) : 2.8003551E-04 9.3479156E-03 energy calculations done at 10.78000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.94000 DelPhi exited at 17:16:16 10.945u 0.487s 0:11.70 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 Mon Oct 10 2011 at 17:16:16 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 = 2711 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.530406 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): -26.35200 32.39900 ymin,ymax (A): -28.10700 29.67500 zmin,zma (A): 25.69900 89.00900 x,y,z range (A): 58.75100 57.78200 63.31001 scale (grids/A): 2.530406 object centre (A): 3.023500 0.7839994 57.35400 number of atom coordinates read : 2711 total number of charged atoms : 2575 net assigned charge : 12.50002 assigned positive charge : 401.2225 centred at (gu) : 91.34842 94.36295 93.43499 assigned negative charge : -388.7234 centred at (gu) : 91.13951 94.84386 92.74121 start vw surface at 0.1100000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 147227 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26245 grid for indexing accessible points = 1.400000 m= 65655 mr = 102025 m= 19084 mr = 50995 m= 3443 mr = 14021 m= 300 mr = 2142 m= 7 mr = 147 m= 0 mr = 0 time to grow re-entrant surface = 0.7600000 no. cavity mid-points inaccessible to solvent = 425 time to turn everything in is 1.280000 number of dielectric boundary points 66386 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 18 iepsmp to db, and charging done at 1.420000 number of grid points assigned charge 20590 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) : 1.686937 object centre at (A) : 3.023500 0.7839994 57.35400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5798453 0.3496523 midg,1,midg; midg,igrid,midg 0.2353328 0.1844062 1,midg,midg; igrid,midg,midg 5.9412993E-02 0.1839046 gauss-seidel spectral radius is 0.9991689 estimated iterations to convergence 274 setup time was (sec) 1.630000 now iterating at: 17:16:19 rms-change max change #iterations 8.398629 302.4775 at 10iterations 4.743489 137.9616 at 20iterations 2.666940 76.38185 at 30iterations 1.499102 38.02999 at 40iterations 0.8362468 19.86528 at 50iterations 0.4665776 11.14705 at 60iterations 0.2601757 5.587532 at 70iterations 0.1447039 3.201347 at 80iterations 8.0517918E-02 1.854532 at 90iterations 4.4740025E-02 0.9295769 at 100iterations 2.4842953E-02 0.5718174 at 110iterations 1.3802956E-02 0.2922697 at 120iterations 7.6725339E-03 0.1628056 at 130iterations 4.2594606E-03 8.7642670E-02 at 140iterations 2.3600224E-03 4.8669338E-02 at 150iterations 1.3121561E-03 2.6262283E-02 at 160iterations 7.2939869E-04 1.5148163E-02 at 170iterations 4.0619465E-04 8.4476471E-03 at 180iterations finished qdiffx linear iterations at : 17:16:36 total time elapsed so far: 19.14000 # loops : 180 mean,max change (kT/e) : 4.0619465E-04 8.4476471E-03 energy calculations done at 19.14000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.30000 DelPhi exited at 17:16:37 19.308u 0.510s 0:20.08 98.6% 0+0k 0+0io 0pf+0w