Sat Oct 8 16:47:42 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 16:47:42 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4441 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 0.5463895 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): 15.68100 78.81600 ymin,ymax (A): 120.1650 185.3200 zmin,zma (A): -1.378000 60.16200 x,y,z range (A): 63.13500 65.15499 61.54000 scale (grids/A): 0.5463895 object centre (A): 47.24850 152.7425 29.39200 number of atom coordinates read : 4441 total number of charged atoms : 4271 net assigned charge : 4.500036 assigned positive charge : 680.6418 centred at (gu) : 91.88224 89.72481 87.60079 assigned negative charge : -676.1448 centred at (gu) : 91.87215 89.66101 87.63372 start vw surface at 0.2200000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 8544 nv = 96 ne = 84 npr = 89077 no. pairs analyzed = 89077 no. exposed pairs = 5593 no. arc points = 38213 no. surface atoms = 1863 nbur = 2578 mkacc time = 0.3000000 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= 335 mr = 4517 m= 1 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6100000 number of dielectric boundary points 4340 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3980 ## 546 charges are in solution ## iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 11401 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1012986E-09 -3.0422324E-11 midg,1,midg; midg,igrid,midg -4.0812240E-10 8.5395085E-10 1,midg,midg; igrid,midg,midg 1.1018458E-10 5.9460453E-10 gauss-seidel spectral radius is 0.9828377 estimated iterations to convergence 63 setup time was (sec) 0.9600000 now iterating at: 16:47:43 rms-change max change #iterations 9.1671973E-02 14.51786 at 10iterations 6.4615747E-03 0.9185734 at 20iterations 9.3927741E-04 0.1322212 at 30iterations 3.0546388E-04 4.0790558E-02 at 40iterations 1.1567405E-04 1.4859915E-02 at 50iterations finished qdiffx linear iterations at : 16:47:47 total time elapsed so far: 4.530000 # loops : 50 mean,max change (kT/e) : 1.1567405E-04 1.4859915E-02 energy calculations done at 4.530000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.740000 DelPhi exited at 16:47:48 4.746u 0.398s 0:05.43 94.4% 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 16:47:48 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4441 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 1.639168 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): 15.68100 78.81600 ymin,ymax (A): 120.1650 185.3200 zmin,zma (A): -1.378000 60.16200 x,y,z range (A): 63.13500 65.15499 61.54000 scale (grids/A): 1.639168 object centre (A): 47.24850 152.7425 29.39200 number of atom coordinates read : 4441 total number of charged atoms : 4271 net assigned charge : 4.500036 assigned positive charge : 680.6418 centred at (gu) : 95.64552 89.17329 82.80158 assigned negative charge : -676.1448 centred at (gu) : 95.61599 88.98276 82.90099 start vw surface at 0.2100000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 95642 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38213 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 30144 mr = 66523 m= 3358 mr = 20382 m= 106 mr = 1713 m= 0 mr = 11 time to grow re-entrant surface = 0.5000000 no. cavity mid-points inaccessible to solvent = 554 time to turn everything in is 0.9700000 number of dielectric boundary points 40621 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 1.110000 number of grid points assigned charge 32655 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) : 0.5463895 object centre at (A) : 47.24850 152.7425 29.39200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.9065451E-03 8.2489634E-03 midg,1,midg; midg,igrid,midg 1.1964106E-02 3.0418182E-02 1,midg,midg; igrid,midg,midg -1.0737637E-02 -1.3258241E-02 gauss-seidel spectral radius is 0.9983449 estimated iterations to convergence 195 setup time was (sec) 1.310000 now iterating at: 16:47:49 rms-change max change #iterations 4.244475 164.8254 at 10iterations 1.831693 62.06767 at 20iterations 0.7944996 24.68274 at 30iterations 0.3447791 10.42033 at 40iterations 0.1498482 4.576330 at 50iterations 6.5062858E-02 2.088221 at 60iterations 2.8431343E-02 0.9577045 at 70iterations 1.2438667E-02 0.4061394 at 80iterations 5.5090501E-03 0.1665039 at 90iterations 2.5072198E-03 8.3086014E-02 at 100iterations 1.1983527E-03 3.8650513E-02 at 110iterations 6.2181923E-04 1.9388199E-02 at 120iterations finished qdiffx linear iterations at : 16:47:59 total time elapsed so far: 10.56000 # loops : 120 mean,max change (kT/e) : 6.2181923E-04 1.9388199E-02 energy calculations done at 10.56000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.77000 DelPhi exited at 16:47:59 10.779u 0.478s 0:11.52 97.5% 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 16:47:59 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4441 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 2.458753 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): 15.68100 78.81600 ymin,ymax (A): 120.1650 185.3200 zmin,zma (A): -1.378000 60.16200 x,y,z range (A): 63.13500 65.15499 61.54000 scale (grids/A): 2.458753 object centre (A): 47.24850 152.7425 29.39200 number of atom coordinates read : 4441 total number of charged atoms : 4271 net assigned charge : 4.500036 assigned positive charge : 680.6418 centred at (gu) : 98.46779 88.75977 79.20216 assigned negative charge : -676.1448 centred at (gu) : 98.42410 88.47398 79.35140 start vw surface at 0.2200000 fill in re-entrant regions at 0.7700000 boundary points on vw surface= 222498 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38213 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 104411 mr = 162879 m= 30011 mr = 82110 m= 5320 mr = 22185 m= 455 mr = 3640 m= 10 mr = 217 m= 0 mr = 0 time to grow re-entrant surface = 1.500000 no. cavity mid-points inaccessible to solvent = 1774 time to turn everything in is 2.430000 number of dielectric boundary points 91674 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 23 iepsmp to db, and charging done at 2.610000 number of grid points assigned charge 34136 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) : 1.639168 object centre at (A) : 47.24850 152.7425 29.39200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.5656782E-02 0.1825510 midg,1,midg; midg,igrid,midg 0.1981893 0.4706582 1,midg,midg; igrid,midg,midg -0.1578467 -0.2295844 gauss-seidel spectral radius is 0.9992200 estimated iterations to convergence 283 setup time was (sec) 2.810000 now iterating at: 16:48:02 rms-change max change #iterations 11.02229 311.5496 at 10iterations 6.436998 138.9798 at 20iterations 3.730081 72.17045 at 30iterations 2.152684 41.35161 at 40iterations 1.238374 22.92137 at 50iterations 0.7093064 14.73605 at 60iterations 0.4050226 7.954584 at 70iterations 0.2308812 4.471740 at 80iterations 0.1317045 2.389725 at 90iterations 7.4769370E-02 1.276106 at 100iterations 4.2617675E-02 0.7394485 at 110iterations 2.4232108E-02 0.4366460 at 120iterations 1.3777227E-02 0.2614689 at 130iterations 7.8456569E-03 0.1364450 at 140iterations 4.4754338E-03 7.8700781E-02 at 150iterations 2.5669832E-03 4.2705536E-02 at 160iterations 1.4889521E-03 2.6453018E-02 at 170iterations 8.7647489E-04 1.5541077E-02 at 180iterations finished qdiffx linear iterations at : 16:48:18 total time elapsed so far: 18.62000 # loops : 180 mean,max change (kT/e) : 8.7647489E-04 1.5541077E-02 energy calculations done at 18.62000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.83000 DelPhi exited at 16:48:19 18.834u 0.500s 0:19.60 98.6% 0+0k 0+0io 0pf+0w