Tue Jan 24 22:49:47 PST 2012 #!/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 Tue Jan 24 2012 at 22:49:47 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 ! Automatically converted by prot2crg.py # of charge parameter records: 994 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4525 !!! WARNING: FAD 995 has a net charge of -2.0000 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: 0.5468006 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): 21.22800 78.49100 ymin,ymax (A): 119.0340 184.1400 zmin,zma (A): -1.855000 59.45200 x,y,z range (A): 57.26300 65.10600 61.30700 scale (grids/A): 0.5468006 object centre (A): 49.85950 151.5870 28.79850 number of atom coordinates read : 4525 total number of charged atoms : 4413 net assigned charge : 3.000040 assigned positive charge : 703.4697 centred at (gu) : 90.73692 89.37933 87.34393 assigned negative charge : -700.4730 centred at (gu) : 90.74437 89.31682 87.37685 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 8662 nv = 96 ne = 84 npr = 91521 no. pairs analyzed = 91521 no. exposed pairs = 5386 no. arc points = 37144 no. surface atoms = 1813 nbur = 2712 mkacc time = 0.1800000 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 = 1.568000 m= 412 mr = 4802 m= 1 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 4 time to turn everything in is 0.3700000 number of dielectric boundary points 4248 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3795 ## 468 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 11581 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0455286E-09 -8.3732264E-11 midg,1,midg; midg,igrid,midg -5.7194965E-10 7.2787470E-10 1,midg,midg; igrid,midg,midg 2.2206886E-10 1.2595835E-10 gauss-seidel spectral radius is 0.9828659 estimated iterations to convergence 63 setup time was (sec) 0.5800000 now iterating at: 22:49:48 rms-change max change #iterations 9.2545904E-02 12.58184 at 10iterations 6.3791606E-03 1.001196 at 20iterations 5.2307750E-04 7.6484680E-02 at 30iterations 9.5464908E-05 1.3900757E-02 at 40iterations 2.7322134E-05 3.5781860E-03 at 50iterations finished qdiffx linear iterations at : 22:49:51 total time elapsed so far: 3.540000 # loops : 50 mean,max change (kT/e) : 2.7322134E-05 3.5781860E-03 energy calculations done at 3.540000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.690000 DelPhi exited at 22:49:51 3.691u 0.168s 0:04.26 90.3% 0+0k 0+46456io 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 Tue Jan 24 2012 at 22:49:51 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 ! Automatically converted by prot2crg.py # of charge parameter records: 994 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4525 !!! WARNING: FAD 995 has a net charge of -2.0000 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: 1.640402 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): 21.22800 78.49100 ymin,ymax (A): 119.0340 184.1400 zmin,zma (A): -1.855000 59.45200 x,y,z range (A): 57.26300 65.10600 61.30700 scale (grids/A): 1.640402 object centre (A): 49.85950 151.5870 28.79850 number of atom coordinates read : 4525 total number of charged atoms : 4413 net assigned charge : 3.000040 assigned positive charge : 703.4697 centred at (gu) : 92.20957 88.13658 82.03082 assigned negative charge : -700.4730 centred at (gu) : 92.23264 87.95023 82.13026 start vw surface at 0.1600000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 97348 reading accessible surface arcs data from file ARCDAT no. of arc points read = 37144 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 30833 mr = 69101 m= 3635 mr = 21453 m= 127 mr = 2000 m= 2 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 149 time to turn everything in is 0.5900000 number of dielectric boundary points 39377 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 444 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 33844 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) : 0.5468006 object centre at (A) : 49.85950 151.5870 28.79850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.1493721E-03 9.2666047E-03 midg,1,midg; midg,igrid,midg 1.0414782E-02 3.0813601E-02 1,midg,midg; igrid,midg,midg -1.4485164E-02 -1.2206241E-02 gauss-seidel spectral radius is 0.9983484 estimated iterations to convergence 195 setup time was (sec) 0.8100000 now iterating at: 22:49:52 rms-change max change #iterations 4.397449 162.8289 at 10iterations 1.906304 66.11017 at 20iterations 0.8269606 26.49962 at 30iterations 0.3605311 10.48192 at 40iterations 0.1572114 5.162025 at 50iterations 6.8204962E-02 1.914948 at 60iterations 2.9752282E-02 0.8519135 at 70iterations 1.2936612E-02 0.3976936 at 80iterations 5.6515541E-03 0.1769218 at 90iterations 2.4731134E-03 7.5142622E-02 at 100iterations 1.0893081E-03 3.2826424E-02 at 110iterations 4.8134642E-04 1.3931274E-02 at 120iterations finished qdiffx linear iterations at : 22:50:00 total time elapsed so far: 8.170000 # loops : 120 mean,max change (kT/e) : 4.8134642E-04 1.3931274E-02 energy calculations done at 8.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.320000 DelPhi exited at 22:50:00 8.327u 0.197s 0:08.81 96.5% 0+0k 0+45552io 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 Tue Jan 24 2012 at 22:50:00 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 ! Automatically converted by prot2crg.py # of charge parameter records: 994 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4525 !!! WARNING: FAD 995 has a net charge of -2.0000 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: 2.460603 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): 21.22800 78.49100 ymin,ymax (A): 119.0340 184.1400 zmin,zma (A): -1.855000 59.45200 x,y,z range (A): 57.26300 65.10600 61.30700 scale (grids/A): 2.460603 object centre (A): 49.85950 151.5870 28.79850 number of atom coordinates read : 4525 total number of charged atoms : 4413 net assigned charge : 3.000040 assigned positive charge : 703.4697 centred at (gu) : 93.31422 87.20469 78.04593 assigned negative charge : -700.4730 centred at (gu) : 93.34905 86.92539 78.19533 start vw surface at 0.1300000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 226827 reading accessible surface arcs data from file ARCDAT no. of arc points read = 37144 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 106413 mr = 168884 m= 31451 mr = 85029 m= 5946 mr = 23930 m= 529 mr = 4172 m= 8 mr = 287 m= 0 mr = 0 time to grow re-entrant surface = 0.9700000 no. cavity mid-points inaccessible to solvent = 527 time to turn everything in is 1.480000 number of dielectric boundary points 88872 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 32 iepsmp to db, and charging done at 1.580000 number of grid points assigned charge 35275 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) : 1.640402 object centre at (A) : 49.85950 151.5870 28.79850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.5047885E-02 0.2037686 midg,1,midg; midg,igrid,midg 0.1576601 0.5397308 1,midg,midg; igrid,midg,midg -0.2259460 -0.2115463 gauss-seidel spectral radius is 0.9992195 estimated iterations to convergence 283 setup time was (sec) 1.720000 now iterating at: 22:50:03 rms-change max change #iterations 11.17272 290.4732 at 10iterations 6.456801 135.3911 at 20iterations 3.705382 74.88292 at 30iterations 2.119730 40.47501 at 40iterations 1.211399 23.77430 at 50iterations 0.6900365 14.05945 at 60iterations 0.3927248 7.274355 at 70iterations 0.2227765 3.710626 at 80iterations 0.1266444 2.406475 at 90iterations 7.1787402E-02 1.333544 at 100iterations 4.0665407E-02 0.7026234 at 110iterations 2.3058223E-02 0.3889728 at 120iterations 1.3062402E-02 0.2397938 at 130iterations 7.4018794E-03 0.1423578 at 140iterations 4.1869213E-03 7.6719746E-02 at 150iterations 2.3714674E-03 4.8301697E-02 at 160iterations 1.3435996E-03 2.3784637E-02 at 170iterations 7.6241873E-04 1.4225960E-02 at 180iterations finished qdiffx linear iterations at : 22:50:15 total time elapsed so far: 13.40000 # loops : 180 mean,max change (kT/e) : 7.6241873E-04 1.4225960E-02 energy calculations done at 13.40000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.54000 DelPhi exited at 22:50:16 13.546u 0.227s 0:15.42 89.2% 0+0k 0+45544io 0pf+0w