Sat Oct 8 13:45:41 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 13:45:41 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3003 !!! WARNING: NDP 318 has a net charge of -3.0000 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: 0.6501570 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): -12.21800 42.53800 ymin,ymax (A): -22.38200 22.58400 zmin,zma (A): -6.360000 48.16300 x,y,z range (A): 54.75600 44.96600 54.52300 scale (grids/A): 0.6501570 object centre (A): 15.16000 0.1009998 20.90150 number of atom coordinates read : 3003 total number of charged atoms : 2857 net assigned charge : -0.9999923 assigned positive charge : 448.5596 centred at (gu) : 89.09605 89.61967 91.19201 assigned negative charge : -449.5603 centred at (gu) : 89.14375 89.49758 91.12497 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 8589 nv = 96 ne = 84 npr = 61845 no. pairs analyzed = 61845 no. exposed pairs = 3515 no. arc points = 24238 no. surface atoms = 1187 nbur = 1816 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 514 mr = 5079 m= 2 mr = 62 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 7 time to turn everything in is 0.3200000 number of dielectric boundary points 3964 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2369 ## 235 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 10281 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.0891463E-08 1.2618819E-08 midg,1,midg; midg,igrid,midg -2.6017332E-08 1.7751541E-08 1,midg,midg; igrid,midg,midg 7.7287696E-09 -8.7170227E-09 gauss-seidel spectral radius is 0.9877751 estimated iterations to convergence 74 setup time was (sec) 0.5300000 now iterating at: 13:45:41 rms-change max change #iterations 0.1741752 21.11785 at 10iterations 1.7891383E-02 2.835190 at 20iterations 1.8615740E-03 0.2373352 at 30iterations 2.1154096E-04 3.2020569E-02 at 40iterations 2.9756447E-05 3.7155151E-03 at 50iterations finished qdiffx linear iterations at : 13:45:44 total time elapsed so far: 2.950000 # loops : 50 mean,max change (kT/e) : 2.9756447E-05 3.7155151E-03 energy calculations done at 2.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.130000 DelPhi exited at 13:45:44 3.134u 0.152s 0:03.58 91.6% 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 13:45:44 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3003 !!! WARNING: NDP 318 has a net charge of -3.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.950471 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): -12.21800 42.53800 ymin,ymax (A): -22.38200 22.58400 zmin,zma (A): -6.360000 48.16300 x,y,z range (A): 54.75600 44.96600 54.52300 scale (grids/A): 1.950471 object centre (A): 15.16000 0.1009998 20.90150 number of atom coordinates read : 3003 total number of charged atoms : 2857 net assigned charge : -0.9999923 assigned positive charge : 448.5596 centred at (gu) : 87.28765 88.85841 93.57536 assigned negative charge : -449.5603 centred at (gu) : 87.43112 88.49236 93.37467 start vw surface at 0.1500000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 93768 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24238 grid for indexing accessible points = 1.400000 m= 36105 mr = 67983 m= 6006 mr = 27730 m= 363 mr = 3867 m= 5 mr = 122 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6200000 number of dielectric boundary points 36545 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 153 iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 22558 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) : 0.6501570 object centre at (A) : 15.16000 0.1009998 20.90150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.8900806E-02 2.2966590E-02 midg,1,midg; midg,igrid,midg -9.0506496E-03 2.2136696E-02 1,midg,midg; igrid,midg,midg -1.3556137E-02 -4.1399472E-03 gauss-seidel spectral radius is 0.9987326 estimated iterations to convergence 222 setup time was (sec) 0.8800000 now iterating at: 13:45:45 rms-change max change #iterations 4.835926 182.5726 at 10iterations 2.341177 65.28119 at 20iterations 1.124945 35.89350 at 30iterations 0.5449427 17.70723 at 40iterations 0.2626273 8.234810 at 50iterations 0.1266519 3.694471 at 60iterations 6.1047185E-02 1.726156 at 70iterations 2.9444344E-02 0.8340111 at 80iterations 1.4238684E-02 0.3694954 at 90iterations 6.8841116E-03 0.2157278 at 100iterations 3.3263650E-03 9.3163729E-02 at 110iterations 1.6144319E-03 4.2671204E-02 at 120iterations finished qdiffx linear iterations at : 13:45:52 total time elapsed so far: 7.120000 # loops : 120 mean,max change (kT/e) : 1.6144319E-03 4.2671204E-02 energy calculations done at 7.120000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.290000 DelPhi exited at 13:45:52 7.296u 0.173s 0:07.76 96.1% 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 Sat Oct 8 2011 at 13:45:52 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3003 !!! WARNING: NDP 318 has a net charge of -3.0000 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: 2.925707 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): -12.21800 42.53800 ymin,ymax (A): -22.38200 22.58400 zmin,zma (A): -6.360000 48.16300 x,y,z range (A): 54.75600 44.96600 54.52300 scale (grids/A): 2.925707 object centre (A): 15.16000 0.1009998 20.90150 number of atom coordinates read : 3003 total number of charged atoms : 2857 net assigned charge : -0.9999923 assigned positive charge : 448.5596 centred at (gu) : 85.93111 88.28759 95.36276 assigned negative charge : -449.5603 centred at (gu) : 86.14667 87.73853 95.06193 start vw surface at 0.1600000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 216846 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24238 grid for indexing accessible points = 1.400000 m= 115757 mr = 164021 m= 44059 mr = 97143 m= 11001 mr = 36322 m= 1555 mr = 8321 m= 78 mr = 1032 m= 1 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.9700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.620000 number of dielectric boundary points 82441 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.740000 number of grid points assigned charge 22852 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) : 1.950471 object centre at (A) : 15.16000 0.1009998 20.90150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.1884818E-02 0.3096409 midg,1,midg; midg,igrid,midg -5.3390335E-02 0.2487850 1,midg,midg; igrid,midg,midg -3.2420620E-02 0.1202785 gauss-seidel spectral radius is 0.9992880 estimated iterations to convergence 296 setup time was (sec) 1.900000 now iterating at: 13:45:54 rms-change max change #iterations 11.16560 495.5792 at 10iterations 6.583457 136.2343 at 20iterations 3.875453 66.53841 at 30iterations 2.268462 39.15589 at 40iterations 1.330645 22.17805 at 50iterations 0.7784454 14.21189 at 60iterations 0.4542323 8.276781 at 70iterations 0.2648549 4.211797 at 80iterations 0.1544283 2.499672 at 90iterations 8.9863956E-02 1.537868 at 100iterations 5.2391920E-02 0.8722554 at 110iterations 3.0461688E-02 0.4992599 at 120iterations 1.7732166E-02 0.2820372 at 130iterations 1.0314084E-02 0.1733987 at 140iterations 6.0073272E-03 9.2433929E-02 at 150iterations 3.4916252E-03 5.7974815E-02 at 160iterations 2.0361531E-03 3.1805038E-02 at 170iterations 1.1898951E-03 1.9162059E-02 at 180iterations finished qdiffx linear iterations at : 13:46:04 total time elapsed so far: 11.45000 # loops : 180 mean,max change (kT/e) : 1.1898951E-03 1.9162059E-02 energy calculations done at 11.45000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.62000 DelPhi exited at 13:46:04 11.622u 0.164s 0:12.09 97.4% 0+0k 0+0io 0pf+0w