Mon Oct 10 17:03:55 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 17:03:56 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3057 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: 0.5759120 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): 3.423000 65.23800 ymin,ymax (A): 13.08800 65.05500 zmin,zma (A): -25.82900 30.78700 x,y,z range (A): 61.81500 51.96700 56.61600 scale (grids/A): 0.5759120 object centre (A): 34.33050 39.07150 2.478999 number of atom coordinates read : 3057 total number of charged atoms : 2912 net assigned charge : -1.499981 assigned positive charge : 461.4170 centred at (gu) : 90.68236 91.43711 90.67105 assigned negative charge : -462.9182 centred at (gu) : 90.69695 91.53674 90.63951 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6735 nv = 96 ne = 84 npr = 61576 no. pairs analyzed = 61576 no. exposed pairs = 3929 no. arc points = 27883 no. surface atoms = 1316 nbur = 1741 mkacc time = 0.1400000 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 = 1.484000 m= 288 mr = 3492 m= 0 mr = 14 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 3517 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2918 ## 366 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 8598 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.5460993E-10 4.4197396E-10 midg,1,midg; midg,igrid,midg 1.2117547E-09 -3.1980476E-09 1,midg,midg; igrid,midg,midg 3.0237798E-11 -6.3856997E-10 gauss-seidel spectral radius is 0.9844530 estimated iterations to convergence 66 setup time was (sec) 0.5700000 now iterating at: 17:03:57 rms-change max change #iterations 9.7224161E-02 17.78603 at 10iterations 7.3181447E-03 1.191684 at 20iterations 5.6721951E-04 9.0831757E-02 at 30iterations 4.4386721E-05 6.5889359E-03 at 40iterations 4.1276967E-06 6.7138672E-04 at 50iterations finished qdiffx linear iterations at : 17:03:59 total time elapsed so far: 2.980000 # loops : 50 mean,max change (kT/e) : 4.1276967E-06 6.7138672E-04 energy calculations done at 2.980000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.170000 DelPhi exited at 17:04:00 3.177u 0.158s 0:04.32 76.8% 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 17:04:00 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 # of charge parameter records: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3057 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: 1.727736 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): 3.423000 65.23800 ymin,ymax (A): 13.08800 65.05500 zmin,zma (A): -25.82900 30.78700 x,y,z range (A): 61.81500 51.96700 56.61600 scale (grids/A): 1.727736 object centre (A): 34.33050 39.07150 2.478999 number of atom coordinates read : 3057 total number of charged atoms : 2912 net assigned charge : -1.499981 assigned positive charge : 461.4170 centred at (gu) : 92.04613 94.31055 92.01244 assigned negative charge : -462.9182 centred at (gu) : 92.09062 94.60982 91.91840 start vw surface at 0.1700000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 73915 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27883 grid for indexing accessible points = 1.400000 m= 23597 mr = 49714 m= 2893 mr = 16478 m= 100 mr = 1625 m= 0 mr = 1 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 878 time to turn everything in is 0.5200000 number of dielectric boundary points 32687 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 290 iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 22555 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) : 0.5759120 object centre at (A) : 34.33050 39.07150 2.478999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.2569328E-04 -1.4689745E-02 midg,1,midg; midg,igrid,midg 3.6281133E-03 -1.5571252E-02 1,midg,midg; igrid,midg,midg 2.5669191E-02 2.2351418E-03 gauss-seidel spectral radius is 0.9984059 estimated iterations to convergence 199 setup time was (sec) 0.7700000 now iterating at: 17:04:01 rms-change max change #iterations 3.837594 172.2455 at 10iterations 1.678323 66.37472 at 20iterations 0.7407287 28.64278 at 30iterations 0.3273143 11.13197 at 40iterations 0.1440863 4.461881 at 50iterations 6.3276611E-02 2.082332 at 60iterations 2.7964795E-02 0.9131012 at 70iterations 1.2300995E-02 0.3797951 at 80iterations 5.4420815E-03 0.1775491 at 90iterations 2.3941877E-03 8.3229065E-02 at 100iterations 1.0601763E-03 3.7006378E-02 at 110iterations 4.6686476E-04 1.5584946E-02 at 120iterations finished qdiffx linear iterations at : 17:04:07 total time elapsed so far: 6.720000 # loops : 120 mean,max change (kT/e) : 4.6686476E-04 1.5584946E-02 energy calculations done at 6.720000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.890000 DelPhi exited at 17:04:08 6.896u 0.189s 0:07.46 94.7% 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 17:04:08 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3057 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.591604 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): 3.423000 65.23800 ymin,ymax (A): 13.08800 65.05500 zmin,zma (A): -25.82900 30.78700 x,y,z range (A): 61.81500 51.96700 56.61600 scale (grids/A): 2.591604 object centre (A): 34.33050 39.07150 2.478999 number of atom coordinates read : 3057 total number of charged atoms : 2912 net assigned charge : -1.499981 assigned positive charge : 461.4170 centred at (gu) : 93.06894 96.46561 93.01833 assigned negative charge : -462.9182 centred at (gu) : 93.13590 96.91471 92.87763 start vw surface at 0.1800000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 171807 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27883 grid for indexing accessible points = 1.400000 m= 79515 mr = 121990 m= 24843 mr = 63009 m= 4840 mr = 18963 m= 394 mr = 3442 m= 11 mr = 195 m= 0 mr = 0 time to grow re-entrant surface = 0.6900001 no. cavity mid-points inaccessible to solvent = 3047 time to turn everything in is 1.230000 number of dielectric boundary points 73811 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 13 iepsmp to db, and charging done at 1.360000 number of grid points assigned charge 23285 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) : 1.727736 object centre at (A) : 34.33050 39.07150 2.478999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.3136368E-02 -0.3121427 midg,1,midg; midg,igrid,midg 3.1494536E-02 -0.1343712 1,midg,midg; igrid,midg,midg 0.6328722 8.4707588E-02 gauss-seidel spectral radius is 0.9992083 estimated iterations to convergence 281 setup time was (sec) 1.500000 now iterating at: 17:04:09 rms-change max change #iterations 9.514017 284.5741 at 10iterations 5.459079 113.1295 at 20iterations 3.117849 72.46523 at 30iterations 1.775596 36.11191 at 40iterations 1.006053 20.08247 at 50iterations 0.5709403 11.52117 at 60iterations 0.3230358 6.743165 at 70iterations 0.1825737 3.643641 at 80iterations 0.1032308 1.950289 at 90iterations 5.8008149E-02 1.092621 at 100iterations 3.2802396E-02 0.6166420 at 110iterations 1.8514872E-02 0.3747578 at 120iterations 1.0404009E-02 0.2099609 at 130iterations 5.8737923E-03 0.1118345 at 140iterations 3.3094939E-03 6.3875914E-02 at 150iterations 1.8637237E-03 3.7223816E-02 at 160iterations 1.0523465E-03 2.0580292E-02 at 170iterations 5.9418089E-04 1.0749817E-02 at 180iterations finished qdiffx linear iterations at : 17:04:19 total time elapsed so far: 10.92000 # loops : 180 mean,max change (kT/e) : 5.9418089E-04 1.0749817E-02 energy calculations done at 10.92000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.09000 DelPhi exited at 17:04:20 11.093u 0.216s 0:12.19 92.6% 0+0k 0+0io 0pf+0w