Sun Oct 9 07:25:52 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 Sun Oct 9 2011 at 07:25:52 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: 245 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1649 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.7177854 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): -7.200000 34.55300 ymin,ymax (A): -2.551000 39.73800 zmin,zma (A): -13.51800 36.07900 x,y,z range (A): 41.75300 42.28900 49.59700 scale (grids/A): 0.7177854 object centre (A): 13.67650 18.59350 11.28050 number of atom coordinates read : 1649 total number of charged atoms : 1512 net assigned charge : -9.499993 assigned positive charge : 240.4202 centred at (gu) : 90.84801 89.66582 90.50270 assigned negative charge : -249.9201 centred at (gu) : 90.70181 90.04642 90.70469 start vw surface at 5.9999999E-02 fill in re-entrant regions at 7.0000000E-02 boundary points on vw surface= 5891 nv = 96 ne = 84 npr = 34490 no. pairs analyzed = 34490 no. exposed pairs = 2116 no. arc points = 15311 no. surface atoms = 714 nbur = 935 mkacc time = 5.9999995E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 406 mr = 3259 m= 1 mr = 66 m= 0 mr = 0 time to grow re-entrant surface = 7.0000000E-02 no. cavity mid-points inaccessible to solvent = 89 time to turn everything in is 0.1400000 number of dielectric boundary points 2973 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1331 ## 89 charges are in solution ## iepsmp to db, and charging done at 0.2100000 number of grid points assigned charge 6215 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.9533732E-09 -2.2534218E-07 midg,1,midg; midg,igrid,midg 8.5929642E-08 -2.7997717E-07 1,midg,midg; igrid,midg,midg -1.4980414E-07 -3.4944062E-08 gauss-seidel spectral radius is 0.9898461 estimated iterations to convergence 81 setup time was (sec) 0.3300000 now iterating at: 07:25:52 rms-change max change #iterations 0.1858204 31.96887 at 10iterations 2.3373112E-02 3.926102 at 20iterations 2.9961022E-03 0.4464722 at 30iterations 3.7153275E-04 5.3169250E-02 at 40iterations 4.7015659E-05 7.5302124E-03 at 50iterations finished qdiffx linear iterations at : 07:25:55 total time elapsed so far: 3.150000 # loops : 50 mean,max change (kT/e) : 4.7015659E-05 7.5302124E-03 energy calculations done at 3.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.290000 DelPhi exited at 07:25:56 3.289u 0.162s 0:03.71 92.7% 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 Sun Oct 9 2011 at 07:25:56 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: 245 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1649 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.153356 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): -7.200000 34.55300 ymin,ymax (A): -2.551000 39.73800 zmin,zma (A): -13.51800 36.07900 x,y,z range (A): 41.75300 42.28900 49.59700 scale (grids/A): 2.153356 object centre (A): 13.67650 18.59350 11.28050 number of atom coordinates read : 1649 total number of charged atoms : 1512 net assigned charge : -9.499993 assigned positive charge : 240.4202 centred at (gu) : 92.54416 88.99759 91.50824 assigned negative charge : -249.9201 centred at (gu) : 92.10558 90.13942 92.11407 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 60931 reading accessible surface arcs data from file ARCDAT no. of arc points read = 15311 grid for indexing accessible points = 1.400000 m= 23893 mr = 40983 m= 4650 mr = 18197 m= 383 mr = 3192 m= 13 mr = 187 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 2182 time to turn everything in is 0.3100000 number of dielectric boundary points 27311 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 51 iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 12032 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) : 0.7177854 object centre at (A) : 13.67650 18.59350 11.28050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.2371733E-02 -7.6093957E-02 midg,1,midg; midg,igrid,midg 9.6266354E-03 -9.0592116E-02 1,midg,midg; igrid,midg,midg -5.9241585E-02 -2.0271797E-02 gauss-seidel spectral radius is 0.9988283 estimated iterations to convergence 231 setup time was (sec) 0.5300000 now iterating at: 07:25:56 rms-change max change #iterations 4.182079 200.4686 at 10iterations 2.054348 72.23582 at 20iterations 1.017348 40.76111 at 30iterations 0.5019553 17.10536 at 40iterations 0.2490823 8.096178 at 50iterations 0.1229690 4.233006 at 60iterations 6.0480621E-02 1.841423 at 70iterations 2.9995458E-02 0.9852610 at 80iterations 1.4852662E-02 0.4934692 at 90iterations 7.3677711E-03 0.2610264 at 100iterations 3.6292400E-03 0.1362419 at 110iterations 1.8030773E-03 5.5887222E-02 at 120iterations finished qdiffx linear iterations at : 07:26:03 total time elapsed so far: 7.460000 # loops : 120 mean,max change (kT/e) : 1.8030773E-03 5.5887222E-02 energy calculations done at 7.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.600000 DelPhi exited at 07:26:04 7.599u 0.184s 0:08.05 96.5% 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 Sun Oct 9 2011 at 07:26:04 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: 245 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1649 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.230034 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): -7.200000 34.55300 ymin,ymax (A): -2.551000 39.73800 zmin,zma (A): -13.51800 36.07900 x,y,z range (A): 41.75300 42.28900 49.59700 scale (grids/A): 3.230034 object centre (A): 13.67650 18.59350 11.28050 number of atom coordinates read : 1649 total number of charged atoms : 1512 net assigned charge : -9.499993 assigned positive charge : 240.4202 centred at (gu) : 93.81634 88.49646 92.26241 assigned negative charge : -249.9201 centred at (gu) : 93.15845 90.20912 93.17113 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 140249 reading accessible surface arcs data from file ARCDAT no. of arc points read = 15311 grid for indexing accessible points = 1.400000 m= 73425 mr = 98836 m= 30859 mr = 60755 m= 8861 mr = 25709 m= 1552 mr = 6987 m= 155 mr = 1110 m= 6 mr = 87 m= 0 mr = 0 time to grow re-entrant surface = 0.4600000 no. cavity mid-points inaccessible to solvent = 7595 time to turn everything in is 0.9400000 number of dielectric boundary points 61623 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.020000 number of grid points assigned charge 12096 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) : 2.153356 object centre at (A) : 13.67650 18.59350 11.28050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3775718 -0.6796010 midg,1,midg; midg,igrid,midg 0.1143808 -0.6449874 1,midg,midg; igrid,midg,midg -0.4464495 -0.1081347 gauss-seidel spectral radius is 0.9992928 estimated iterations to convergence 297 setup time was (sec) 1.160000 now iterating at: 07:26:05 rms-change max change #iterations 9.316082 373.0803 at 10iterations 5.418490 137.9303 at 20iterations 3.161702 61.36977 at 30iterations 1.839638 35.92951 at 40iterations 1.074942 21.34780 at 50iterations 0.6243981 11.85107 at 60iterations 0.3635262 7.415976 at 70iterations 0.2111778 4.017524 at 80iterations 0.1226772 2.234072 at 90iterations 7.1306035E-02 1.323358 at 100iterations 4.1402683E-02 0.8037949 at 110iterations 2.4034288E-02 0.4581789 at 120iterations 1.3965532E-02 0.3007202 at 130iterations 8.1000701E-03 0.1676583 at 140iterations 4.7153686E-03 8.5318565E-02 at 150iterations 2.7339302E-03 5.2646637E-02 at 160iterations 1.5941586E-03 2.9420853E-02 at 170iterations 9.2423393E-04 1.7345428E-02 at 180iterations finished qdiffx linear iterations at : 07:26:16 total time elapsed so far: 12.15000 # loops : 180 mean,max change (kT/e) : 9.2423393E-04 1.7345428E-02 energy calculations done at 12.15000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.28000 DelPhi exited at 07:26:17 12.284u 0.216s 0:12.77 97.8% 0+0k 0+0io 0pf+0w