Tue Oct 11 06:14:16 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 06:14:16 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 = 2019 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.7298971 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): 26.58600 72.12000 ymin,ymax (A): 44.26200 82.43400 zmin,zma (A): -60.83200 -12.05800 x,y,z range (A): 45.53400 38.17200 48.77399 scale (grids/A): 0.7298971 object centre (A): 49.35300 63.34800 -36.44500 number of atom coordinates read : 2019 total number of charged atoms : 1889 net assigned charge : 4.500006 assigned positive charge : 303.3131 centred at (gu) : 89.94799 89.27967 88.53824 assigned negative charge : -298.8132 centred at (gu) : 90.08737 89.39214 88.52701 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7450 nv = 96 ne = 84 npr = 40637 no. pairs analyzed = 40637 no. exposed pairs = 2575 no. arc points = 17353 no. surface atoms = 875 nbur = 1144 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 547 mr = 4251 m= 5 mr = 104 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2500000 number of dielectric boundary points 3647 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1464 ## 122 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 7909 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.0813570E-08 5.4803248E-08 midg,1,midg; midg,igrid,midg 1.7010339E-07 -2.0757195E-08 1,midg,midg; igrid,midg,midg 1.7018753E-07 -4.5098520E-08 gauss-seidel spectral radius is 0.9902068 estimated iterations to convergence 82 setup time was (sec) 0.5600000 now iterating at: 06:14:17 rms-change max change #iterations 0.2273649 29.39772 at 10iterations 3.0022357E-02 4.067488 at 20iterations 4.1931919E-03 0.5846863 at 30iterations 7.8962772E-04 0.1009560 at 40iterations 2.3921242E-04 2.8045654E-02 at 50iterations finished qdiffx linear iterations at : 06:14:21 total time elapsed so far: 4.250000 # loops : 50 mean,max change (kT/e) : 2.3921242E-04 2.8045654E-02 energy calculations done at 4.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.430000 DelPhi exited at 06:14:22 4.437u 0.391s 0:05.12 94.1% 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 06:14:22 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 = 2019 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.189692 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): 26.58600 72.12000 ymin,ymax (A): 44.26200 82.43400 zmin,zma (A): -60.83200 -12.05800 x,y,z range (A): 45.53400 38.17200 48.77399 scale (grids/A): 2.189692 object centre (A): 49.35300 63.34800 -36.44500 number of atom coordinates read : 2019 total number of charged atoms : 1889 net assigned charge : 4.500006 assigned positive charge : 303.3131 centred at (gu) : 89.84403 87.83891 85.61473 assigned negative charge : -298.8132 centred at (gu) : 90.26220 88.17657 85.58105 start vw surface at 0.1100000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 77946 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17353 grid for indexing accessible points = 1.400000 m= 33168 mr = 54969 m= 7110 mr = 25345 m= 740 mr = 4881 m= 16 mr = 357 m= 0 mr = 0 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6700000 number of dielectric boundary points 33428 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 54 iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 15019 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) : 0.7298971 object centre at (A) : 49.35300 63.34800 -36.44500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9209702E-03 1.9926261E-02 midg,1,midg; midg,igrid,midg 4.3363269E-02 -8.3773639E-03 1,midg,midg; igrid,midg,midg 4.9007408E-02 3.0314254E-02 gauss-seidel spectral radius is 0.9988888 estimated iterations to convergence 237 setup time was (sec) 0.9600000 now iterating at: 06:14:23 rms-change max change #iterations 4.732979 183.8019 at 10iterations 2.377215 72.54181 at 20iterations 1.207976 35.01535 at 30iterations 0.6121632 17.38207 at 40iterations 0.3082520 9.101229 at 50iterations 0.1555962 4.907387 at 60iterations 7.8785598E-02 2.347740 at 70iterations 3.9916039E-02 1.188515 at 80iterations 2.0418946E-02 0.6073961 at 90iterations 1.0453342E-02 0.3007860 at 100iterations 5.4107411E-03 0.1679535 at 110iterations 2.8949738E-03 8.9835882E-02 at 120iterations finished qdiffx linear iterations at : 06:14:32 total time elapsed so far: 10.45000 # loops : 120 mean,max change (kT/e) : 2.8949738E-03 8.9835882E-02 energy calculations done at 10.45000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.62000 DelPhi exited at 06:14:33 10.629u 0.452s 0:11.58 95.5% 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 Tue Oct 11 2011 at 06:14:33 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 = 2019 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 3.284537 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): 26.58600 72.12000 ymin,ymax (A): 44.26200 82.43400 zmin,zma (A): -60.83200 -12.05800 x,y,z range (A): 45.53400 38.17200 48.77399 scale (grids/A): 3.284537 object centre (A): 49.35300 63.34800 -36.44500 number of atom coordinates read : 2019 total number of charged atoms : 1889 net assigned charge : 4.500006 assigned positive charge : 303.3131 centred at (gu) : 89.76596 86.75849 83.42209 assigned negative charge : -298.8132 centred at (gu) : 90.39337 87.26485 83.37162 start vw surface at 0.1200000 fill in re-entrant regions at 0.8100000 boundary points on vw surface= 179133 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17353 grid for indexing accessible points = 1.400000 m= 100615 mr = 132310 m= 44312 mr = 83805 m= 13820 mr = 36667 m= 2855 mr = 10729 m= 365 mr = 2061 m= 10 mr = 251 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 1.180000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.110000 number of dielectric boundary points 75288 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.240000 number of grid points assigned charge 15112 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) : 2.189692 object centre at (A) : 49.35300 63.34800 -36.44500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.7713845E-02 2.0998355E-02 midg,1,midg; midg,igrid,midg 0.3563907 -5.8973514E-02 1,midg,midg; igrid,midg,midg 0.4042288 0.4196070 gauss-seidel spectral radius is 0.9993117 estimated iterations to convergence 301 setup time was (sec) 2.430000 now iterating at: 06:14:36 rms-change max change #iterations 10.42943 400.1536 at 10iterations 6.265730 188.2379 at 20iterations 3.745903 73.72107 at 30iterations 2.233917 40.11133 at 40iterations 1.331964 26.19090 at 50iterations 0.7879906 14.11857 at 60iterations 0.4673992 8.398102 at 70iterations 0.2771344 5.298500 at 80iterations 0.1638949 2.805673 at 90iterations 9.6602403E-02 1.556706 at 100iterations 5.7186581E-02 1.003157 at 110iterations 3.3985253E-02 0.6256180 at 120iterations 2.0388888E-02 0.3549156 at 130iterations 1.2399315E-02 0.2436228 at 140iterations 7.7909408E-03 0.1502876 at 150iterations 5.1349020E-03 9.8335266E-02 at 160iterations 3.6103469E-03 6.5505981E-02 at 170iterations 2.7236794E-03 4.5516968E-02 at 180iterations finished qdiffx linear iterations at : 06:14:52 total time elapsed so far: 18.28000 # loops : 180 mean,max change (kT/e) : 2.7236794E-03 4.5516968E-02 energy calculations done at 18.28000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.45000 DelPhi exited at 06:14:53 18.458u 0.481s 0:19.25 98.3% 0+0k 0+0io 0pf+0w