Sat Oct 8 16:38:46 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 Sat Oct 8 2011 at 16:38:46 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: 364 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4549 !!! WARNING: GLM 204 has a net charge of -0.0940 !!! WARNING: FAD 994 has a net charge of -2.0000 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: 0.5440680 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): 17.02900 79.38500 ymin,ymax (A): 119.2800 184.7130 zmin,zma (A): -1.664000 59.80400 x,y,z range (A): 62.35600 65.43300 61.46800 scale (grids/A): 0.5440680 object centre (A): 48.20700 151.9965 29.07000 number of atom coordinates read : 4549 total number of charged atoms : 4388 net assigned charge : 2.906037 assigned positive charge : 701.0436 centred at (gu) : 91.66435 89.25535 87.30894 assigned negative charge : -698.1410 centred at (gu) : 91.62625 89.17274 87.32506 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 8781 nv = 96 ne = 84 npr = 89944 no. pairs analyzed = 89944 no. exposed pairs = 5524 no. arc points = 38655 no. surface atoms = 1864 nbur = 2685 mkacc time = 0.2300000 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= 429 mr = 4771 m= 3 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 14 time to turn everything in is 0.4800000 number of dielectric boundary points 4418 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3991 ## 530 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 11584 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.1821920E-10 5.8698849E-12 midg,1,midg; midg,igrid,midg -7.7339340E-10 7.8430318E-10 1,midg,midg; igrid,midg,midg -1.3359776E-10 7.9658952E-10 gauss-seidel spectral radius is 0.9827032 estimated iterations to convergence 63 setup time was (sec) 0.7700000 now iterating at: 16:38:47 rms-change max change #iterations 9.0670794E-02 13.45907 at 10iterations 6.2936782E-03 0.9401608 at 20iterations 6.2638253E-04 8.1943512E-02 at 30iterations 1.5614874E-04 2.0592690E-02 at 40iterations 4.8763286E-05 6.7522526E-03 at 50iterations finished qdiffx linear iterations at : 16:38:51 total time elapsed so far: 4.480000 # loops : 50 mean,max change (kT/e) : 4.8763286E-05 6.7522526E-03 energy calculations done at 4.480000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.630000 DelPhi exited at 16:38:51 4.638u 0.417s 0:05.32 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 Sat Oct 8 2011 at 16:38:51 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: 364 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4549 !!! WARNING: GLM 204 has a net charge of -0.0940 !!! WARNING: FAD 994 has a net charge of -2.0000 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: 1.632204 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): 17.02900 79.38500 ymin,ymax (A): 119.2800 184.7130 zmin,zma (A): -1.664000 59.80400 x,y,z range (A): 62.35600 65.43300 61.46800 scale (grids/A): 1.632204 object centre (A): 48.20700 151.9965 29.07000 number of atom coordinates read : 4549 total number of charged atoms : 4388 net assigned charge : 2.906037 assigned positive charge : 701.0436 centred at (gu) : 94.99211 87.76512 81.92587 assigned negative charge : -698.1410 centred at (gu) : 94.87862 87.51811 81.97479 start vw surface at 0.1700000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 98406 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38655 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 31336 mr = 68849 m= 3640 mr = 21926 m= 118 mr = 1993 m= 0 mr = 12 time to grow re-entrant surface = 0.4200000 no. cavity mid-points inaccessible to solvent = 1278 time to turn everything in is 0.7900000 number of dielectric boundary points 40720 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 529 ## 6 charges are in solution ## iepsmp to db, and charging done at 0.9600000 number of grid points assigned charge 33615 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) : 0.5440680 object centre at (A) : 48.20700 151.9965 29.07000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.7868229E-03 8.4232781E-03 midg,1,midg; midg,igrid,midg 1.4887474E-02 2.9963620E-02 1,midg,midg; igrid,midg,midg -1.0590576E-02 -1.5282081E-02 gauss-seidel spectral radius is 0.9983375 estimated iterations to convergence 195 setup time was (sec) 1.140000 now iterating at: 16:38:53 rms-change max change #iterations 4.294818 247.8880 at 10iterations 1.854861 82.97446 at 20iterations 0.7991235 36.08823 at 30iterations 0.3476809 10.60262 at 40iterations 0.1503700 4.816963 at 50iterations 6.5467983E-02 2.463326 at 60iterations 2.8296951E-02 0.8819275 at 70iterations 1.2318174E-02 0.3615422 at 80iterations 5.3688167E-03 0.1834860 at 90iterations 2.3626895E-03 7.5724602E-02 at 100iterations 1.0493966E-03 3.5447657E-02 at 110iterations 4.7386100E-04 1.6265869E-02 at 120iterations finished qdiffx linear iterations at : 16:39:02 total time elapsed so far: 10.77000 # loops : 120 mean,max change (kT/e) : 4.7386100E-04 1.6265869E-02 energy calculations done at 10.77000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.94000 DelPhi exited at 16:39:03 10.940u 0.461s 0:11.69 97.5% 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 Sat Oct 8 2011 at 16:39:03 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: 364 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4549 !!! WARNING: GLM 204 has a net charge of -0.0940 !!! WARNING: FAD 994 has a net charge of -2.0000 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: 2.448306 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): 17.02900 79.38500 ymin,ymax (A): 119.2800 184.7130 zmin,zma (A): -1.664000 59.80400 x,y,z range (A): 62.35600 65.43300 61.46800 scale (grids/A): 2.448306 object centre (A): 48.20700 151.9965 29.07000 number of atom coordinates read : 4549 total number of charged atoms : 4388 net assigned charge : 2.906037 assigned positive charge : 701.0436 centred at (gu) : 97.48781 86.64731 77.88858 assigned negative charge : -698.1410 centred at (gu) : 97.31787 86.27710 77.96211 start vw surface at 0.1600000 fill in re-entrant regions at 0.6200000 boundary points on vw surface= 228974 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38655 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 108266 mr = 168502 m= 32409 mr = 86589 m= 6069 mr = 24835 m= 476 mr = 4223 m= 10 mr = 241 m= 0 mr = 0 time to grow re-entrant surface = 1.230000 no. cavity mid-points inaccessible to solvent = 4409 time to turn everything in is 1.980000 number of dielectric boundary points 91814 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 25 iepsmp to db, and charging done at 2.140000 number of grid points assigned charge 35045 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) : 1.632204 object centre at (A) : 48.20700 151.9965 29.07000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.1835575E-02 0.1802704 midg,1,midg; midg,igrid,midg 0.2266705 0.4909798 1,midg,midg; igrid,midg,midg -0.1477746 -0.2527841 gauss-seidel spectral radius is 0.9992151 estimated iterations to convergence 282 setup time was (sec) 2.330000 now iterating at: 16:39:06 rms-change max change #iterations 11.04485 389.5892 at 10iterations 6.391041 151.9805 at 20iterations 3.672479 70.71963 at 30iterations 2.104505 45.99542 at 40iterations 1.204231 25.59300 at 50iterations 0.6851217 12.11912 at 60iterations 0.3892996 6.953262 at 70iterations 0.2207430 4.070646 at 80iterations 0.1251822 2.267773 at 90iterations 7.0995495E-02 1.219509 at 100iterations 4.0182319E-02 0.7297519 at 110iterations 2.2781910E-02 0.3698101 at 120iterations 1.2854792E-02 0.2169914 at 130iterations 7.2871484E-03 0.1246207 at 140iterations 4.1210535E-03 7.0319176E-02 at 150iterations 2.3324969E-03 3.8740635E-02 at 160iterations 1.3175806E-03 2.2033691E-02 at 170iterations 7.4690790E-04 1.3245583E-02 at 180iterations finished qdiffx linear iterations at : 16:39:22 total time elapsed so far: 18.90000 # loops : 180 mean,max change (kT/e) : 7.4690790E-04 1.3245583E-02 energy calculations done at 18.90000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.08000 DelPhi exited at 16:39:23 19.081u 0.506s 0:19.84 98.6% 0+0k 0+0io 0pf+0w