Wed Dec 21 14:22:38 PST 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 Wed Dec 21 2011 at 14:22:39 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1966 !!! WARNING: ASH 25 has a net charge of -0.3190 !!! WARNING: ASH 125 has a net charge of -0.3190 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6543636 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): -6.329000 34.24800 ymin,ymax (A): -3.422000 48.88900 zmin,zma (A): -23.51000 30.89400 x,y,z range (A): 40.57700 52.31100 54.40400 scale (grids/A): 0.6543636 object centre (A): 13.95950 22.73350 3.692000 number of atom coordinates read : 1966 total number of charged atoms : 1832 net assigned charge : 3.362005 assigned positive charge : 292.6019 centred at (gu) : 91.00651 92.33155 89.99550 assigned negative charge : -289.2403 centred at (gu) : 91.12196 92.48545 89.92955 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 5697 nv = 96 ne = 84 npr = 40486 no. pairs analyzed = 40486 no. exposed pairs = 2437 no. arc points = 17064 no. surface atoms = 818 nbur = 1148 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 317 mr = 3209 m= 3 mr = 43 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 25 time to turn everything in is 0.2500000 number of dielectric boundary points 2765 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1736 ## 163 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 6684 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.1443543E-10 1.6246918E-08 midg,1,midg; midg,igrid,midg 1.6713088E-08 -1.9929503E-08 1,midg,midg; igrid,midg,midg 1.8155633E-08 -8.5499421E-09 gauss-seidel spectral radius is 0.9878384 estimated iterations to convergence 74 setup time was (sec) 0.5400000 now iterating at: 14:22:41 rms-change max change #iterations 0.1431545 26.28919 at 10iterations 1.5200263E-02 2.037354 at 20iterations 1.5506305E-03 0.2454147 at 30iterations 1.5769384E-04 2.4488449E-02 at 40iterations 1.6682166E-05 2.7236938E-03 at 50iterations finished qdiffx linear iterations at : 14:22:46 total time elapsed so far: 6.000000 # loops : 50 mean,max change (kT/e) : 1.6682166E-05 2.7236938E-03 energy calculations done at 6.000000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.180000 DelPhi exited at 14:22:51 6.185u 0.502s 0:12.56 53.1% 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 Wed Dec 21 2011 at 14:22:52 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1966 !!! WARNING: ASH 25 has a net charge of -0.3190 !!! WARNING: ASH 125 has a net charge of -0.3190 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.963091 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): -6.329000 34.24800 ymin,ymax (A): -3.422000 48.88900 zmin,zma (A): -23.51000 30.89400 x,y,z range (A): 40.57700 52.31100 54.40400 scale (grids/A): 1.963091 object centre (A): 13.95950 22.73350 3.692000 number of atom coordinates read : 1966 total number of charged atoms : 1832 net assigned charge : 3.362005 assigned positive charge : 292.6019 centred at (gu) : 93.01949 96.99477 89.98646 assigned negative charge : -289.2403 centred at (gu) : 93.36607 97.45657 89.78901 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 61459 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17064 grid for indexing accessible points = 1.400000 m= 22500 mr = 42701 m= 3520 mr = 17149 m= 190 mr = 2337 m= 0 mr = 58 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 2180 time to turn everything in is 0.5200000 number of dielectric boundary points 25424 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 99 iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 14482 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) : 0.6543636 object centre at (A) : 13.95950 22.73350 3.692000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.7459895E-02 1.8428987E-02 midg,1,midg; midg,igrid,midg 3.9469633E-02 -1.1543019E-02 1,midg,midg; igrid,midg,midg 1.3503278E-02 -4.0625213E-03 gauss-seidel spectral radius is 0.9986328 estimated iterations to convergence 214 setup time was (sec) 0.9400000 now iterating at: 14:22:54 rms-change max change #iterations 3.828651 170.5823 at 10iterations 1.800357 62.64788 at 20iterations 0.8418056 30.31351 at 30iterations 0.3928474 13.51713 at 40iterations 0.1834789 5.951606 at 50iterations 8.6082079E-02 2.872276 at 60iterations 4.0200770E-02 1.344271 at 70iterations 1.8826237E-02 0.6582794 at 80iterations 8.8100536E-03 0.2782135 at 90iterations 4.1095586E-03 0.1349542 at 100iterations 1.9294852E-03 7.0854187E-02 at 110iterations 9.0226351E-04 3.0739784E-02 at 120iterations finished qdiffx linear iterations at : 14:23:12 total time elapsed so far: 18.79000 # loops : 120 mean,max change (kT/e) : 9.0226351E-04 3.0739784E-02 energy calculations done at 18.79000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.96000 DelPhi exited at 14:23:13 18.964u 0.702s 0:21.65 90.8% 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 Wed Dec 21 2011 at 14:23:15 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1966 !!! WARNING: ASH 25 has a net charge of -0.3190 !!! WARNING: ASH 125 has a net charge of -0.3190 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: 2.944636 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): -6.329000 34.24800 ymin,ymax (A): -3.422000 48.88900 zmin,zma (A): -23.51000 30.89400 x,y,z range (A): 40.57700 52.31100 54.40400 scale (grids/A): 2.944636 object centre (A): 13.95950 22.73350 3.692000 number of atom coordinates read : 1966 total number of charged atoms : 1832 net assigned charge : 3.362005 assigned positive charge : 292.6019 centred at (gu) : 94.52917 100.4921 89.97973 assigned negative charge : -289.2403 centred at (gu) : 95.04923 101.1849 89.68345 start vw surface at 0.1300000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 141726 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17064 grid for indexing accessible points = 1.400000 m= 72603 mr = 102914 m= 26951 mr = 60467 m= 6568 mr = 22390 m= 914 mr = 5102 m= 41 mr = 599 m= 0 mr = 15 time to grow re-entrant surface = 0.7900000 no. cavity mid-points inaccessible to solvent = 7116 time to turn everything in is 1.380000 number of dielectric boundary points 57316 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.520000 number of grid points assigned charge 14656 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) : 1.963091 object centre at (A) : 13.95950 22.73350 3.692000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.7956010 6.4706363E-02 midg,1,midg; midg,igrid,midg 0.3711502 -0.1512570 1,midg,midg; igrid,midg,midg 0.1038416 -1.4367608E-02 gauss-seidel spectral radius is 0.9992462 estimated iterations to convergence 287 setup time was (sec) 1.820000 now iterating at: 14:23:17 rms-change max change #iterations 8.874767 428.1130 at 10iterations 5.090904 133.1261 at 20iterations 2.901717 60.22307 at 30iterations 1.657470 35.44550 at 40iterations 0.9473476 22.29235 at 50iterations 0.5395522 10.39914 at 60iterations 0.3075069 6.021517 at 70iterations 0.1750550 3.612937 at 80iterations 9.9980570E-02 1.999318 at 90iterations 5.6958936E-02 1.090981 at 100iterations 3.2435007E-02 0.6270747 at 110iterations 1.8549133E-02 0.3621073 at 120iterations 1.0557837E-02 0.2009029 at 130iterations 6.0219564E-03 0.1362000 at 140iterations 3.4298978E-03 7.5325012E-02 at 150iterations 1.9612100E-03 3.8421631E-02 at 160iterations 1.1188132E-03 2.0330429E-02 at 170iterations 6.3671859E-04 1.2497902E-02 at 180iterations finished qdiffx linear iterations at : 14:23:46 total time elapsed so far: 30.75000 # loops : 180 mean,max change (kT/e) : 6.3671859E-04 1.2497902E-02 energy calculations done at 30.75000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 30.91000 DelPhi exited at 14:23:47 30.918u 0.735s 0:32.03 98.7% 0+0k 0+0io 0pf+0w