Tue Oct 11 07:53:01 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 Tue Oct 11 2011 at 07:53:01 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 = 2380 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: 0.6384276 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): -1.975000 53.78700 ymin,ymax (A): -22.76100 26.18600 zmin,zma (A): 9.101000 53.62900 x,y,z range (A): 55.76200 48.94700 44.52800 scale (grids/A): 0.6384276 object centre (A): 25.90600 1.712500 31.36500 number of atom coordinates read : 2380 total number of charged atoms : 2244 net assigned charge : 5.500007 assigned positive charge : 357.6723 centred at (gu) : 88.79932 89.33002 90.24123 assigned negative charge : -352.1728 centred at (gu) : 88.81541 89.26488 90.05960 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6534 nv = 96 ne = 84 npr = 47866 no. pairs analyzed = 47866 no. exposed pairs = 2901 no. arc points = 20610 no. surface atoms = 984 nbur = 1396 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 356 mr = 3631 m= 1 mr = 49 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3211 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2090 ## 231 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 7858 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.0528029E-08 2.7034172E-08 midg,1,midg; midg,igrid,midg 1.0841088E-09 1.2310558E-08 1,midg,midg; igrid,midg,midg 1.1927918E-08 4.7111417E-09 gauss-seidel spectral radius is 0.9872699 estimated iterations to convergence 72 setup time was (sec) 0.6100000 now iterating at: 07:53:02 rms-change max change #iterations 0.1385950 20.64444 at 10iterations 1.3720498E-02 1.907089 at 20iterations 1.3896696E-03 0.2597733 at 30iterations 1.5119673E-04 2.3277283E-02 at 40iterations 1.9053530E-05 2.7256012E-03 at 50iterations finished qdiffx linear iterations at : 07:53:05 total time elapsed so far: 3.880000 # loops : 50 mean,max change (kT/e) : 1.9053530E-05 2.7256012E-03 energy calculations done at 3.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.040000 DelPhi exited at 07:53:05 4.048u 0.267s 0:04.63 92.8% 0+0k 0+0io 6pf+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 Oct 11 2011 at 07:53:05 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2380 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: 1.915283 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): -1.975000 53.78700 ymin,ymax (A): -22.76100 26.18600 zmin,zma (A): 9.101000 53.62900 x,y,z range (A): 55.76200 48.94700 44.52800 scale (grids/A): 1.915283 object centre (A): 25.90600 1.712500 31.36500 number of atom coordinates read : 2380 total number of charged atoms : 2244 net assigned charge : 5.500007 assigned positive charge : 357.6723 centred at (gu) : 86.39756 87.99002 90.72338 assigned negative charge : -352.1728 centred at (gu) : 86.44617 87.79443 90.17866 start vw surface at 0.1400000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 70066 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20610 grid for indexing accessible points = 1.400000 m= 26424 mr = 48702 m= 3984 mr = 19794 m= 226 mr = 2437 m= 1 mr = 92 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6200000 number of dielectric boundary points 29676 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 166 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 17656 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) : 0.6384276 object centre at (A) : 25.90600 1.712500 31.36500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9799545E-02 3.6850296E-02 midg,1,midg; midg,igrid,midg -3.0503881E-03 5.7659848E-03 1,midg,midg; igrid,midg,midg 2.1181576E-02 3.0611861E-02 gauss-seidel spectral radius is 0.9986299 estimated iterations to convergence 214 setup time was (sec) 0.9200000 now iterating at: 07:53:07 rms-change max change #iterations 4.054965 183.9864 at 10iterations 1.892046 71.97626 at 20iterations 0.8928631 30.47395 at 30iterations 0.4168313 16.87547 at 40iterations 0.1957110 7.569061 at 50iterations 9.1657378E-02 3.383465 at 60iterations 4.3000683E-02 1.454214 at 70iterations 2.0102300E-02 0.6417236 at 80iterations 9.4018904E-03 0.3141803 at 90iterations 4.4235345E-03 0.1412239 at 100iterations 2.0752563E-03 7.0359707E-02 at 110iterations 9.7499572E-04 3.1444550E-02 at 120iterations finished qdiffx linear iterations at : 07:53:15 total time elapsed so far: 9.120000 # loops : 120 mean,max change (kT/e) : 9.7499572E-04 3.1444550E-02 energy calculations done at 9.120000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.300000 DelPhi exited at 07:53:16 9.302u 0.314s 0:10.18 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 Tue Oct 11 2011 at 07:53:16 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 = 2380 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: 2.872924 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): -1.975000 53.78700 ymin,ymax (A): -22.76100 26.18600 zmin,zma (A): 9.101000 53.62900 x,y,z range (A): 55.76200 48.94700 44.52800 scale (grids/A): 2.872924 object centre (A): 25.90600 1.712500 31.36500 number of atom coordinates read : 2380 total number of charged atoms : 2244 net assigned charge : 5.500007 assigned positive charge : 357.6723 centred at (gu) : 84.59624 86.98483 91.08498 assigned negative charge : -352.1728 centred at (gu) : 84.66921 86.69161 90.26794 start vw surface at 0.1600000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 161763 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20610 grid for indexing accessible points = 1.400000 m= 84341 mr = 117436 m= 31125 mr = 69948 m= 6989 mr = 25146 m= 1028 mr = 5154 m= 61 mr = 699 m= 0 mr = 30 time to grow re-entrant surface = 0.9900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.650000 number of dielectric boundary points 66894 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.800000 number of grid points assigned charge 17948 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) : 1.915283 object centre at (A) : 25.90600 1.712500 31.36500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2799972 0.3911834 midg,1,midg; midg,igrid,midg -4.5794863E-02 -1.0815876E-02 1,midg,midg; igrid,midg,midg 8.3560050E-02 0.2667607 gauss-seidel spectral radius is 0.9992494 estimated iterations to convergence 288 setup time was (sec) 1.970000 now iterating at: 07:53:18 rms-change max change #iterations 9.435783 431.7086 at 10iterations 5.460616 140.9474 at 20iterations 3.159633 82.68203 at 30iterations 1.816046 36.60082 at 40iterations 1.044056 19.91513 at 50iterations 0.5994997 14.24660 at 60iterations 0.3438809 6.483258 at 70iterations 0.1969842 3.833906 at 80iterations 0.1127823 2.060154 at 90iterations 6.4682864E-02 1.287197 at 100iterations 3.7101105E-02 0.6808767 at 110iterations 2.1217542E-02 0.3919849 at 120iterations 1.2171141E-02 0.2394562 at 130iterations 6.9872355E-03 0.1359968 at 140iterations 4.0148008E-03 7.3784590E-02 at 150iterations 2.3166572E-03 4.4050217E-02 at 160iterations 1.3378352E-03 2.4261475E-02 at 170iterations 7.7813002E-04 1.4966965E-02 at 180iterations finished qdiffx linear iterations at : 07:53:31 total time elapsed so far: 15.34000 # loops : 180 mean,max change (kT/e) : 7.7813002E-04 1.4966965E-02 energy calculations done at 15.34000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.52000 DelPhi exited at 07:53:32 15.519u 0.281s 0:16.09 98.1% 0+0k 0+0io 0pf+0w