Sat Oct 8 13:13:47 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 Sat Oct 8 2011 at 13:13:47 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3006 !!! WARNING: GLU 646 has a net charge of -2.0000 !!! WARNING: TPO 1 has a net charge of -1.2740 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5975159 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): -5.293000 44.21400 ymin,ymax (A): -23.46900 27.42500 zmin,zma (A): -8.170000 51.41000 x,y,z range (A): 49.50700 50.89400 59.58000 scale (grids/A): 0.5975159 object centre (A): 19.46050 1.978000 21.62000 number of atom coordinates read : 3006 total number of charged atoms : 2858 net assigned charge : 0.2260241 assigned positive charge : 450.5539 centred at (gu) : 88.71350 89.97323 89.97253 assigned negative charge : -450.3289 centred at (gu) : 88.63181 90.02218 90.21488 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 7176 nv = 96 ne = 84 npr = 61081 no. pairs analyzed = 61081 no. exposed pairs = 3823 no. arc points = 26500 no. surface atoms = 1277 nbur = 1729 mkacc time = 0.2000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 339 mr = 3932 m= 1 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 44 time to turn everything in is 0.4500000 number of dielectric boundary points 3567 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2749 ## 281 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 9000 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.4273362E-09 -9.5472785E-09 midg,1,midg; midg,igrid,midg 2.0636546E-09 -1.7688515E-09 1,midg,midg; igrid,midg,midg -4.1656225E-09 2.4646074E-09 gauss-seidel spectral radius is 0.9855398 estimated iterations to convergence 68 setup time was (sec) 0.7600000 now iterating at: 13:13:48 rms-change max change #iterations 0.1171164 15.67023 at 10iterations 1.0372567E-02 1.697395 at 20iterations 1.6369831E-03 0.3085384 at 30iterations 6.5668870E-04 0.1355076 at 40iterations 3.0174074E-04 6.2517166E-02 at 50iterations finished qdiffx linear iterations at : 13:13:52 total time elapsed so far: 4.680000 # loops : 50 mean,max change (kT/e) : 3.0174074E-04 6.2517166E-02 energy calculations done at 4.680000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.900000 DelPhi exited at 13:13:52 4.906u 0.445s 0:05.63 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 Sat Oct 8 2011 at 13:13:53 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3006 !!! WARNING: GLU 646 has a net charge of -2.0000 !!! WARNING: TPO 1 has a net charge of -1.2740 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: 1.792548 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): -5.293000 44.21400 ymin,ymax (A): -23.46900 27.42500 zmin,zma (A): -8.170000 51.41000 x,y,z range (A): 49.50700 50.89400 59.58000 scale (grids/A): 1.792548 object centre (A): 19.46050 1.978000 21.62000 number of atom coordinates read : 3006 total number of charged atoms : 2858 net assigned charge : 0.2260241 assigned positive charge : 450.5539 centred at (gu) : 86.13972 89.91888 89.91695 assigned negative charge : -450.3289 centred at (gu) : 85.89455 90.06615 90.64436 start vw surface at 0.1600000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 78034 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26500 grid for indexing accessible points = 1.400000 m= 27435 mr = 54197 m= 3572 mr = 19922 m= 161 mr = 1986 m= 2 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.4100000 no. cavity mid-points inaccessible to solvent = 2575 time to turn everything in is 0.7900000 number of dielectric boundary points 33078 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 238 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.9300000 number of grid points assigned charge 22324 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) : 0.5975159 object centre at (A) : 19.46050 1.978000 21.62000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.8188396E-02 -2.5901332E-02 midg,1,midg; midg,igrid,midg 5.6436863E-03 2.7466665E-03 1,midg,midg; igrid,midg,midg -3.7319693E-03 3.4915523E-03 gauss-seidel spectral radius is 0.9985074 estimated iterations to convergence 205 setup time was (sec) 1.140000 now iterating at: 13:13:54 rms-change max change #iterations 4.088499 183.5031 at 10iterations 1.842983 72.16491 at 20iterations 0.8364987 26.69467 at 30iterations 0.3780369 10.95418 at 40iterations 0.1709549 5.389078 at 50iterations 7.7415988E-02 2.437426 at 60iterations 3.5259999E-02 1.170868 at 70iterations 1.6129004E-02 0.5079470 at 80iterations 7.5552398E-03 0.2960606 at 90iterations 3.7472153E-03 0.1389065 at 100iterations 2.0531360E-03 9.0353012E-02 at 110iterations 1.2853093E-03 5.1625252E-02 at 120iterations finished qdiffx linear iterations at : 13:14:05 total time elapsed so far: 11.54000 # loops : 120 mean,max change (kT/e) : 1.2853093E-03 5.1625252E-02 energy calculations done at 11.54000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.75000 DelPhi exited at 13:14:05 11.753u 0.528s 0:12.56 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 Sat Oct 8 2011 at 13:14:05 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3006 !!! WARNING: GLU 646 has a net charge of -2.0000 !!! WARNING: TPO 1 has a net charge of -1.2740 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: 2.688822 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): -5.293000 44.21400 ymin,ymax (A): -23.46900 27.42500 zmin,zma (A): -8.170000 51.41000 x,y,z range (A): 49.50700 50.89400 59.58000 scale (grids/A): 2.688822 object centre (A): 19.46050 1.978000 21.62000 number of atom coordinates read : 3006 total number of charged atoms : 2858 net assigned charge : 0.2260241 assigned positive charge : 450.5539 centred at (gu) : 84.20951 89.87798 89.87515 assigned negative charge : -450.3289 centred at (gu) : 83.84168 90.09907 90.96638 start vw surface at 0.1500000 fill in re-entrant regions at 0.6500000 boundary points on vw surface= 180654 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26500 grid for indexing accessible points = 1.400000 m= 90415 mr = 131420 m= 30030 mr = 73657 m= 6122 mr = 23503 m= 685 mr = 4325 m= 22 mr = 343 m= 0 mr = 2 time to grow re-entrant surface = 1.260000 no. cavity mid-points inaccessible to solvent = 8611 time to turn everything in is 2.050000 number of dielectric boundary points 74678 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 2.220000 number of grid points assigned charge 22854 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) : 1.792548 object centre at (A) : 19.46050 1.978000 21.62000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1089164 -0.2445008 midg,1,midg; midg,igrid,midg 7.2308548E-02 6.5942399E-02 1,midg,midg; igrid,midg,midg -1.4256082E-02 -1.7667001E-02 gauss-seidel spectral radius is 0.9992318 estimated iterations to convergence 285 setup time was (sec) 2.450000 now iterating at: 13:14:08 rms-change max change #iterations 9.952143 326.6608 at 10iterations 5.795372 157.5351 at 20iterations 3.342858 76.70960 at 30iterations 1.920465 42.46423 at 40iterations 1.105981 23.84713 at 50iterations 0.6331145 12.37780 at 60iterations 0.3621862 7.158852 at 70iterations 0.2070756 4.089994 at 80iterations 0.1183987 2.269444 at 90iterations 6.7514412E-02 1.306076 at 100iterations 3.8659327E-02 0.7246552 at 110iterations 2.2128344E-02 0.4329033 at 120iterations 1.2777891E-02 0.2533083 at 130iterations 7.4690636E-03 0.1495132 at 140iterations 4.5050606E-03 9.9487305E-02 at 150iterations 2.8634216E-03 6.9601059E-02 at 160iterations 1.9537660E-03 4.7027588E-02 at 170iterations 1.4454052E-03 3.6464691E-02 at 180iterations finished qdiffx linear iterations at : 13:14:28 total time elapsed so far: 22.60000 # loops : 180 mean,max change (kT/e) : 1.4454052E-03 3.6464691E-02 energy calculations done at 22.60000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 22.84000 DelPhi exited at 13:14:29 22.847u 0.545s 0:23.71 98.6% 0+0k 0+0io 0pf+0w