Mon Oct 10 11:17:53 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 11:17:53 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2117 !!! WARNING: LYS 224 has a net charge of -0.2720 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: 0.7481349 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): -20.87800 24.19700 ymin,ymax (A): -7.979000 36.25600 zmin,zma (A): -3.497000 44.08800 x,y,z range (A): 45.07500 44.23500 47.58500 scale (grids/A): 0.7481349 object centre (A): 1.659500 14.13850 20.29550 number of atom coordinates read : 2117 total number of charged atoms : 1978 net assigned charge : -6.271980 assigned positive charge : 317.0999 centred at (gu) : 89.06214 90.42535 90.25663 assigned negative charge : -323.3720 centred at (gu) : 89.08475 90.51218 90.43062 start vw surface at 0.1200000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 8170 nv = 96 ne = 84 npr = 43829 no. pairs analyzed = 43829 no. exposed pairs = 2753 no. arc points = 19132 no. surface atoms = 929 nbur = 1188 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 595 mr = 4506 m= 5 mr = 116 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 64 time to turn everything in is 0.2400000 number of dielectric boundary points 4148 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1490 ## 107 charges are in solution ## iepsmp to db, and charging done at 0.3400000 number of grid points assigned charge 8536 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.2390876E-08 -3.6106533E-07 midg,1,midg; midg,igrid,midg -2.4916947E-08 -2.5549488E-07 1,midg,midg; igrid,midg,midg -1.2168294E-07 -1.3339420E-07 gauss-seidel spectral radius is 0.9906904 estimated iterations to convergence 84 setup time was (sec) 0.4700000 now iterating at: 11:17:54 rms-change max change #iterations 0.2581507 38.57629 at 10iterations 3.5553847E-02 4.516500 at 20iterations 4.8898049E-03 0.6577470 at 30iterations 6.6573860E-04 8.7285995E-02 at 40iterations 9.2650327E-05 1.3717651E-02 at 50iterations finished qdiffx linear iterations at : 11:17:57 total time elapsed so far: 3.090000 # loops : 50 mean,max change (kT/e) : 9.2650327E-05 1.3717651E-02 energy calculations done at 3.090000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.250000 DelPhi exited at 11:17:57 3.258u 0.232s 0:03.79 91.8% 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 Mon Oct 10 2011 at 11:17:57 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2117 !!! WARNING: LYS 224 has a net charge of -0.2720 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: 2.244405 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): -20.87800 24.19700 ymin,ymax (A): -7.979000 36.25600 zmin,zma (A): -3.497000 44.08800 x,y,z range (A): 45.07500 44.23500 47.58500 scale (grids/A): 2.244405 object centre (A): 1.659500 14.13850 20.29550 number of atom coordinates read : 2117 total number of charged atoms : 1978 net assigned charge : -6.271980 assigned positive charge : 317.0999 centred at (gu) : 87.18632 91.27607 90.76997 assigned negative charge : -323.3720 centred at (gu) : 87.25414 91.53648 91.29186 start vw surface at 0.1400000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 85664 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19132 grid for indexing accessible points = 1.400000 m= 34590 mr = 58929 m= 7585 mr = 26094 m= 836 mr = 5174 m= 33 mr = 459 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 1832 time to turn everything in is 0.6300000 number of dielectric boundary points 38052 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 35 iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 15782 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) : 0.7481349 object centre at (A) : 1.659500 14.13850 20.29550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.6620453E-03 -0.1399923 midg,1,midg; midg,igrid,midg -2.6558338E-02 -3.2689530E-02 1,midg,midg; igrid,midg,midg -1.9145895E-02 -1.0642461E-02 gauss-seidel spectral radius is 0.9989471 estimated iterations to convergence 244 setup time was (sec) 0.9300000 now iterating at: 11:17:58 rms-change max change #iterations 5.214346 218.6391 at 10iterations 2.664183 80.15730 at 20iterations 1.363969 39.00599 at 30iterations 0.6992339 19.14306 at 40iterations 0.3588625 10.51223 at 50iterations 0.1844293 5.426379 at 60iterations 9.4470032E-02 2.923548 at 70iterations 4.8319459E-02 1.428172 at 80iterations 2.4817200E-02 0.6737576 at 90iterations 1.2785577E-02 0.3330472 at 100iterations 6.5439055E-03 0.1880248 at 110iterations 3.3618561E-03 9.5973969E-02 at 120iterations finished qdiffx linear iterations at : 11:18:05 total time elapsed so far: 7.540000 # loops : 120 mean,max change (kT/e) : 3.3618561E-03 9.5973969E-02 energy calculations done at 7.540000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.680000 DelPhi exited at 11:18:06 7.686u 0.247s 0:08.35 94.8% 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 Mon Oct 10 2011 at 11:18:06 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2117 !!! WARNING: LYS 224 has a net charge of -0.2720 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: 3.366607 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): -20.87800 24.19700 ymin,ymax (A): -7.979000 36.25600 zmin,zma (A): -3.497000 44.08800 x,y,z range (A): 45.07500 44.23500 47.58500 scale (grids/A): 3.366607 object centre (A): 1.659500 14.13850 20.29550 number of atom coordinates read : 2117 total number of charged atoms : 1978 net assigned charge : -6.271980 assigned positive charge : 317.0999 centred at (gu) : 85.77949 91.91405 91.15497 assigned negative charge : -323.3720 centred at (gu) : 85.88127 92.30478 91.93788 start vw surface at 0.1300000 fill in re-entrant regions at 0.9000000 boundary points on vw surface= 197224 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19132 grid for indexing accessible points = 1.400000 m= 105441 mr = 142064 m= 45432 mr = 87025 m= 14622 mr = 37482 m= 3487 mr = 11478 m= 467 mr = 2582 m= 23 mr = 273 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.9900000 no. cavity mid-points inaccessible to solvent = 5925 time to turn everything in is 2.020000 number of dielectric boundary points 85788 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.150000 number of grid points assigned charge 15824 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) : 2.244405 object centre at (A) : 1.659500 14.13850 20.29550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.2638164E-02 -1.224926 midg,1,midg; midg,igrid,midg -0.2465728 -0.1719760 1,midg,midg; igrid,midg,midg -0.2036531 -0.1587057 gauss-seidel spectral radius is 0.9993269 estimated iterations to convergence 304 setup time was (sec) 2.330000 now iterating at: 11:18:08 rms-change max change #iterations 11.22375 306.3916 at 10iterations 6.644648 144.6570 at 20iterations 3.941810 92.31287 at 30iterations 2.330539 42.71445 at 40iterations 1.375804 23.38285 at 50iterations 0.8129335 13.31749 at 60iterations 0.4796608 7.989370 at 70iterations 0.2823116 4.505798 at 80iterations 0.1665304 2.653073 at 90iterations 9.8304540E-02 1.697189 at 100iterations 5.7860967E-02 0.8730011 at 110iterations 3.4062479E-02 0.6416216 at 120iterations 2.0071093E-02 0.3512230 at 130iterations 1.1828879E-02 0.1745553 at 140iterations 6.9800653E-03 0.1145847 at 150iterations 4.1120308E-03 7.0598602E-02 at 160iterations 2.4225053E-03 3.8683891E-02 at 170iterations 1.4267237E-03 2.3479462E-02 at 180iterations finished qdiffx linear iterations at : 11:18:19 total time elapsed so far: 13.07000 # loops : 180 mean,max change (kT/e) : 1.4267237E-03 2.3479462E-02 energy calculations done at 13.07000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.24000 DelPhi exited at 11:18:20 13.241u 0.282s 0:13.81 97.9% 0+0k 0+0io 0pf+0w