Sat Oct 8 11:45:01 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 11:45:01 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 = 4433 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: 0.5614079 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): -27.25700 35.12900 ymin,ymax (A): 34.69100 98.10300 zmin,zma (A): 30.99300 90.89100 x,y,z range (A): 62.38600 63.41201 59.89799 scale (grids/A): 0.5614079 object centre (A): 3.935999 66.39700 60.94200 number of atom coordinates read : 4433 total number of charged atoms : 4273 net assigned charge : -7.499951 assigned positive charge : 665.9361 centred at (gu) : 90.79838 88.44627 88.71106 assigned negative charge : -673.4392 centred at (gu) : 90.67815 88.50404 88.86689 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 8841 nv = 96 ne = 84 npr = 93636 no. pairs analyzed = 93636 no. exposed pairs = 4949 no. arc points = 33719 no. surface atoms = 1686 nbur = 2747 mkacc time = 0.1600000 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= 392 mr = 5116 m= 1 mr = 33 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 126 time to turn everything in is 0.3000000 number of dielectric boundary points 4085 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3541 ## 443 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 11835 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.4615192E-09 -2.7106446E-09 midg,1,midg; midg,igrid,midg 1.6825036E-10 -1.3332555E-09 1,midg,midg; igrid,midg,midg -2.5171158E-09 1.4371130E-09 gauss-seidel spectral radius is 0.9837333 estimated iterations to convergence 64 setup time was (sec) 0.5300000 now iterating at: 11:45:02 rms-change max change #iterations 0.1048097 14.29375 at 10iterations 8.1342533E-03 1.101841 at 20iterations 1.0136184E-03 0.1749229 at 30iterations 2.5027775E-04 4.5619965E-02 at 40iterations 7.7296005E-05 1.2123108E-02 at 50iterations finished qdiffx linear iterations at : 11:45:05 total time elapsed so far: 3.730000 # loops : 50 mean,max change (kT/e) : 7.7296005E-05 1.2123108E-02 energy calculations done at 3.730000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.870000 DelPhi exited at 11:45:06 3.877u 0.227s 0:04.55 89.8% 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 11:45:06 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 = 4433 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: 1.684224 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): -27.25700 35.12900 ymin,ymax (A): 34.69100 98.10300 zmin,zma (A): 30.99300 90.89100 x,y,z range (A): 62.38600 63.41201 59.89799 scale (grids/A): 1.684224 object centre (A): 3.935999 66.39700 60.94200 number of atom coordinates read : 4433 total number of charged atoms : 4273 net assigned charge : -7.499951 assigned positive charge : 665.9361 centred at (gu) : 92.39389 85.33774 86.13172 assigned negative charge : -673.4392 centred at (gu) : 92.03391 85.51168 86.60029 start vw surface at 0.1200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 99576 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33719 grid for indexing accessible points = 1.400000 m= 33216 mr = 72363 m= 4091 mr = 24359 m= 125 mr = 2417 m= 2 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 7016 time to turn everything in is 0.5000000 number of dielectric boundary points 37851 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 404 iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 33006 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) : 0.5614079 object centre at (A) : 3.935999 66.39700 60.94200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.8439710E-02 -2.4525942E-02 midg,1,midg; midg,igrid,midg 1.4064212E-02 -7.7725626E-03 1,midg,midg; igrid,midg,midg -2.6261359E-02 2.3388430E-02 gauss-seidel spectral radius is 0.9984205 estimated iterations to convergence 200 setup time was (sec) 0.7600000 now iterating at: 11:45:07 rms-change max change #iterations 4.498175 186.1734 at 10iterations 1.982793 62.86419 at 20iterations 0.8798363 25.10140 at 30iterations 0.3904457 12.00244 at 40iterations 0.1729131 5.181799 at 50iterations 7.6951213E-02 2.397594 at 60iterations 3.4047812E-02 1.053673 at 70iterations 1.5198913E-02 0.4314313 at 80iterations 6.7873537E-03 0.2085028 at 90iterations 3.0526014E-03 8.2607269E-02 at 100iterations 1.3919547E-03 3.7483215E-02 at 110iterations 6.5226952E-04 1.9016266E-02 at 120iterations finished qdiffx linear iterations at : 11:45:16 total time elapsed so far: 10.21000 # loops : 120 mean,max change (kT/e) : 6.5226952E-04 1.9016266E-02 energy calculations done at 10.21000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.34000 DelPhi exited at 11:45:17 10.347u 0.275s 0:10.96 96.8% 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 11:45:17 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 = 4433 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: 2.526335 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): -27.25700 35.12900 ymin,ymax (A): 34.69100 98.10300 zmin,zma (A): 30.99300 90.89100 x,y,z range (A): 62.38600 63.41201 59.89799 scale (grids/A): 2.526335 object centre (A): 3.935999 66.39700 60.94200 number of atom coordinates read : 4433 total number of charged atoms : 4273 net assigned charge : -7.499951 assigned positive charge : 665.9361 centred at (gu) : 93.59036 83.00612 84.19749 assigned negative charge : -673.4392 centred at (gu) : 93.05070 83.26736 84.90025 start vw surface at 0.1200000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 231433 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33719 grid for indexing accessible points = 1.400000 m= 113533 mr = 175632 m= 35028 mr = 93465 m= 6759 mr = 27667 m= 557 mr = 4980 m= 8 mr = 306 m= 0 mr = 0 time to grow re-entrant surface = 0.7399999 no. cavity mid-points inaccessible to solvent = 22973 time to turn everything in is 1.340000 number of dielectric boundary points 85268 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 26 iepsmp to db, and charging done at 1.480000 number of grid points assigned charge 34166 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) : 1.684224 object centre at (A) : 3.935999 66.39700 60.94200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5394622 -0.2940155 midg,1,midg; midg,igrid,midg 0.2728749 -0.1190624 1,midg,midg; igrid,midg,midg -0.3500983 0.2059144 gauss-seidel spectral radius is 0.9992256 estimated iterations to convergence 284 setup time was (sec) 1.700000 now iterating at: 11:45:19 rms-change max change #iterations 11.19389 324.9161 at 10iterations 6.465452 128.1177 at 20iterations 3.718360 84.06815 at 30iterations 2.133993 38.50920 at 40iterations 1.221286 20.33216 at 50iterations 0.6972292 11.09060 at 60iterations 0.3975689 7.380142 at 70iterations 0.2265466 3.987381 at 80iterations 0.1292011 2.100581 at 90iterations 7.3423937E-02 1.408192 at 100iterations 4.1782264E-02 0.7422142 at 110iterations 2.3777481E-02 0.4055786 at 120iterations 1.3546909E-02 0.2298775 at 130iterations 7.7293129E-03 0.1255531 at 140iterations 4.4167833E-03 8.5371971E-02 at 150iterations 2.5372230E-03 4.1934967E-02 at 160iterations 1.4675907E-03 2.3895264E-02 at 170iterations 8.5968361E-04 1.4532089E-02 at 180iterations finished qdiffx linear iterations at : 11:45:34 total time elapsed so far: 17.28000 # loops : 180 mean,max change (kT/e) : 8.5968361E-04 1.4532089E-02 energy calculations done at 17.28000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.41000 DelPhi exited at 11:45:35 17.416u 0.365s 0:18.15 97.9% 0+0k 0+0io 0pf+0w