Tue Oct 11 07:03:00 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 Tue Oct 11 2011 at 07:03:00 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: 258 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3037 !!! WARNING: UMP 501 has a net charge of -0.1000 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: 0.5505893 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): -59.18100 5.477000 ymin,ymax (A): -15.41100 42.22100 zmin,zma (A): 5.808000 54.13600 x,y,z range (A): 64.65800 57.63200 48.32800 scale (grids/A): 0.5505893 object centre (A): -26.85200 13.40500 29.97200 number of atom coordinates read : 3037 total number of charged atoms : 2893 net assigned charge : -4.099982 assigned positive charge : 444.8854 centred at (gu) : 87.94849 89.56016 90.49945 assigned negative charge : -448.9860 centred at (gu) : 88.11544 89.67549 90.53480 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 5982 nv = 96 ne = 84 npr = 62390 no. pairs analyzed = 62390 no. exposed pairs = 3813 no. arc points = 27044 no. surface atoms = 1289 nbur = 1748 mkacc time = 0.1100000 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= 222 mr = 3104 m= 0 mr = 4 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2200000 number of dielectric boundary points 3096 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2665 ## 329 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 7724 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.1282527E-11 -6.9695977E-10 midg,1,midg; midg,igrid,midg 6.3360933E-10 -1.1330832E-09 1,midg,midg; igrid,midg,midg 1.6265628E-09 -1.0204847E-09 gauss-seidel spectral radius is 0.9829967 estimated iterations to convergence 63 setup time was (sec) 0.4100000 now iterating at: 07:03:00 rms-change max change #iterations 7.8141026E-02 14.65641 at 10iterations 5.3821877E-03 0.8425808 at 20iterations 4.3085840E-04 7.4106216E-02 at 30iterations 6.0859591E-05 1.6048431E-02 at 40iterations 1.3617802E-05 3.7727356E-03 at 50iterations finished qdiffx linear iterations at : 07:03:03 total time elapsed so far: 3.300000 # loops : 50 mean,max change (kT/e) : 1.3617802E-05 3.7727356E-03 energy calculations done at 3.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.440000 DelPhi exited at 07:03:04 3.442u 0.177s 0:03.99 90.4% 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 07:03:04 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: 258 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3037 !!! WARNING: UMP 501 has a net charge of -0.1000 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: 1.651768 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): -59.18100 5.477000 ymin,ymax (A): -15.41100 42.22100 zmin,zma (A): 5.808000 54.13600 x,y,z range (A): 64.65800 57.63200 48.32800 scale (grids/A): 1.651768 object centre (A): -26.85200 13.40500 29.97200 number of atom coordinates read : 3037 total number of charged atoms : 2893 net assigned charge : -4.099982 assigned positive charge : 444.8854 centred at (gu) : 83.84479 88.67974 91.49757 assigned negative charge : -448.9860 centred at (gu) : 84.34606 89.02613 91.60382 start vw surface at 0.1100000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 66304 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27044 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 20345 mr = 44743 m= 2081 mr = 14248 m= 57 mr = 1076 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 849 time to turn everything in is 0.3400000 number of dielectric boundary points 28717 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 248 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 22284 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) : 0.5505893 object centre at (A) : -26.85200 13.40500 29.97200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.8278558E-03 8.0416212E-03 midg,1,midg; midg,igrid,midg -5.7845362E-05 -2.7031606E-02 1,midg,midg; igrid,midg,midg -3.5196659E-03 -2.2413956E-02 gauss-seidel spectral radius is 0.9982370 estimated iterations to convergence 189 setup time was (sec) 0.5600000 now iterating at: 07:03:04 rms-change max change #iterations 3.400331 147.0599 at 10iterations 1.429381 55.63599 at 20iterations 0.6044909 21.77356 at 30iterations 0.2556218 8.508885 at 40iterations 0.1078919 3.824539 at 50iterations 4.5606390E-02 1.660591 at 60iterations 1.9203745E-02 0.6700897 at 70iterations 8.0909766E-03 0.2890840 at 80iterations 3.4195122E-03 0.1163297 at 90iterations 1.4551147E-03 5.4008484E-02 at 100iterations 6.1298761E-04 2.0236880E-02 at 110iterations 2.6079229E-04 9.1557503E-03 at 120iterations finished qdiffx linear iterations at : 07:03:12 total time elapsed so far: 7.640000 # loops : 120 mean,max change (kT/e) : 2.6079229E-04 9.1557503E-03 energy calculations done at 7.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.770000 DelPhi exited at 07:03:12 7.776u 0.176s 0:08.50 93.4% 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 07:03:12 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: 258 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3037 !!! WARNING: UMP 501 has a net charge of -0.1000 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: 2.477652 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): -59.18100 5.477000 ymin,ymax (A): -15.41100 42.22100 zmin,zma (A): 5.808000 54.13600 x,y,z range (A): 64.65800 57.63200 48.32800 scale (grids/A): 2.477652 object centre (A): -26.85200 13.40500 29.97200 number of atom coordinates read : 3037 total number of charged atoms : 2893 net assigned charge : -4.099982 assigned positive charge : 444.8854 centred at (gu) : 80.76696 88.01941 92.24617 assigned negative charge : -448.9860 centred at (gu) : 81.51897 88.53897 92.40569 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 154005 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27044 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 70195 mr = 109460 m= 20361 mr = 55900 m= 3212 mr = 15553 m= 242 mr = 2178 m= 3 mr = 120 m= 0 mr = 0 time to grow re-entrant surface = 0.4500000 no. cavity mid-points inaccessible to solvent = 3116 time to turn everything in is 0.8000000 number of dielectric boundary points 64807 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 19 iepsmp to db, and charging done at 0.8900000 number of grid points assigned charge 23115 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) : 1.651768 object centre at (A) : -26.85200 13.40500 29.97200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.7652504E-02 0.1451404 midg,1,midg; midg,igrid,midg 5.2313235E-02 -0.4802604 1,midg,midg; igrid,midg,midg -0.1216111 -0.4571096 gauss-seidel spectral radius is 0.9991574 estimated iterations to convergence 272 setup time was (sec) 1.030000 now iterating at: 07:03:13 rms-change max change #iterations 8.778931 363.0823 at 10iterations 4.945076 117.9315 at 20iterations 2.768871 59.35379 at 30iterations 1.546003 33.61002 at 40iterations 0.8599290 19.03308 at 50iterations 0.4776549 11.51060 at 60iterations 0.2651335 5.377491 at 70iterations 0.1472524 3.198908 at 80iterations 8.1447221E-02 1.780991 at 90iterations 4.5114093E-02 0.9618816 at 100iterations 2.4972674E-02 0.4903088 at 110iterations 1.3809547E-02 0.2644768 at 120iterations 7.6288991E-03 0.1445541 at 130iterations 4.2270939E-03 8.0088615E-02 at 140iterations 2.3364110E-03 4.7470093E-02 at 150iterations 1.2927764E-03 2.6466370E-02 at 160iterations 7.1326888E-04 1.5368044E-02 at 170iterations 3.9480792E-04 7.5715333E-03 at 180iterations finished qdiffx linear iterations at : 07:03:25 total time elapsed so far: 12.25000 # loops : 180 mean,max change (kT/e) : 3.9480792E-04 7.5715333E-03 energy calculations done at 12.25000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.38000 DelPhi exited at 07:03:25 12.383u 0.211s 0:12.88 97.7% 0+0k 0+0io 0pf+0w