Wed Dec 28 11:03:19 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 28 2011 at 11:03:21 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1959 !!! WARNING: ASH 25 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6017274 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): -8.713000 50.45000 ymin,ymax (A): 8.852000 49.31200 zmin,zma (A): -4.266000 38.83600 x,y,z range (A): 59.16300 40.46000 43.10200 scale (grids/A): 0.6017274 object centre (A): 20.86850 29.08200 17.28500 number of atom coordinates read : 1959 total number of charged atoms : 1826 net assigned charge : 4.681012 assigned positive charge : 290.5440 centred at (gu) : 89.89632 89.41501 90.48302 assigned negative charge : -285.8632 centred at (gu) : 89.88524 89.30172 90.63889 start vw surface at 0.1800000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 4751 nv = 96 ne = 84 npr = 40451 no. pairs analyzed = 40451 no. exposed pairs = 2525 no. arc points = 17605 no. surface atoms = 854 nbur = 1105 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 220 mr = 2555 m= 0 mr = 13 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 2403 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1851 ## 226 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 5868 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.8381007E-09 -2.6154130E-09 midg,1,midg; midg,igrid,midg -1.2550322E-09 4.6824127E-09 1,midg,midg; igrid,midg,midg 1.8998849E-09 2.4298026E-09 gauss-seidel spectral radius is 0.9856514 estimated iterations to convergence 68 setup time was (sec) 0.5200000 now iterating at: 11:03:23 rms-change max change #iterations 9.8290205E-02 18.34302 at 10iterations 8.0832792E-03 1.590164 at 20iterations 6.9949840E-04 0.1283607 at 30iterations 5.8269852E-05 1.0133743E-02 at 40iterations 4.9740338E-06 9.7751617E-04 at 50iterations finished qdiffx linear iterations at : 11:03:25 total time elapsed so far: 3.240000 # loops : 50 mean,max change (kT/e) : 4.9740338E-06 9.7751617E-04 energy calculations done at 3.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.790000 DelPhi exited at 11:03:29 3.792u 0.587s 0:07.63 57.2% 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 28 2011 at 11:03:29 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1959 !!! WARNING: ASH 25 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.805182 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): -8.713000 50.45000 ymin,ymax (A): 8.852000 49.31200 zmin,zma (A): -4.266000 38.83600 x,y,z range (A): 59.16300 40.46000 43.10200 scale (grids/A): 1.805182 object centre (A): 20.86850 29.08200 17.28500 number of atom coordinates read : 1959 total number of charged atoms : 1826 net assigned charge : 4.681012 assigned positive charge : 290.5440 centred at (gu) : 89.68903 88.24506 91.44908 assigned negative charge : -285.8632 centred at (gu) : 89.65575 87.90534 91.91671 start vw surface at 0.1500000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 51748 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17605 grid for indexing accessible points = 1.400000 m= 16978 mr = 35058 m= 1953 mr = 12436 m= 90 mr = 1044 m= 0 mr = 19 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4300000 number of dielectric boundary points 22212 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 188 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 14283 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) : 0.6017274 object centre at (A) : 20.86850 29.08200 17.28500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0820661E-02 -4.9475553E-03 midg,1,midg; midg,igrid,midg 1.7820218E-03 6.1584413E-03 1,midg,midg; igrid,midg,midg 3.6596943E-02 3.5840053E-02 gauss-seidel spectral radius is 0.9984062 estimated iterations to convergence 199 setup time was (sec) 0.7500000 now iterating at: 11:03:30 rms-change max change #iterations 3.224613 159.8747 at 10iterations 1.417501 55.82002 at 20iterations 0.6229854 24.98531 at 30iterations 0.2747573 10.47404 at 40iterations 0.1211724 5.156750 at 50iterations 5.3347450E-02 2.079769 at 60iterations 2.3441616E-02 1.031220 at 70iterations 1.0343368E-02 0.4263794 at 80iterations 4.5508081E-03 0.1747961 at 90iterations 2.0032355E-03 7.8428268E-02 at 100iterations 8.8026602E-04 3.5308838E-02 at 110iterations 3.8907724E-04 1.4108658E-02 at 120iterations finished qdiffx linear iterations at : 11:03:37 total time elapsed so far: 7.280000 # loops : 120 mean,max change (kT/e) : 3.8907724E-04 1.4108658E-02 energy calculations done at 7.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.830000 DelPhi exited at 11:03:40 7.830u 0.619s 0:10.81 78.0% 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 28 2011 at 11:03:40 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1959 !!! WARNING: ASH 25 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.707773 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): -8.713000 50.45000 ymin,ymax (A): 8.852000 49.31200 zmin,zma (A): -4.266000 38.83600 x,y,z range (A): 59.16300 40.46000 43.10200 scale (grids/A): 2.707773 object centre (A): 20.86850 29.08200 17.28500 number of atom coordinates read : 1959 total number of charged atoms : 1826 net assigned charge : 4.681012 assigned positive charge : 290.5440 centred at (gu) : 89.53346 87.36766 92.17356 assigned negative charge : -285.8632 centred at (gu) : 89.48370 86.85794 92.87514 start vw surface at 0.1900000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 119874 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17605 grid for indexing accessible points = 1.400000 m= 57118 mr = 85151 m= 17825 mr = 46387 m= 3154 mr = 14271 m= 358 mr = 2213 m= 17 mr = 209 m= 0 mr = 4 time to grow re-entrant surface = 0.4900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9500000 number of dielectric boundary points 50111 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.060000 number of grid points assigned charge 14606 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) : 1.805182 object centre at (A) : 20.86850 29.08200 17.28500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1015386 -3.8653422E-02 midg,1,midg; midg,igrid,midg 5.1651713E-02 4.9428262E-02 1,midg,midg; igrid,midg,midg 0.4576056 0.3570947 gauss-seidel spectral radius is 0.9991769 estimated iterations to convergence 275 setup time was (sec) 1.230000 now iterating at: 11:03:42 rms-change max change #iterations 7.863406 276.1190 at 10iterations 4.486665 153.6782 at 20iterations 2.529742 59.29754 at 30iterations 1.415577 32.13018 at 40iterations 0.7922078 17.67492 at 50iterations 0.4432602 10.03268 at 60iterations 0.2470975 5.562383 at 70iterations 0.1374542 3.005497 at 80iterations 7.6677546E-02 1.684625 at 90iterations 4.2833164E-02 1.047995 at 100iterations 2.3787817E-02 0.5330162 at 110iterations 1.3273080E-02 0.2857966 at 120iterations 7.3760129E-03 0.1546526 at 130iterations 4.0942561E-03 9.1127396E-02 at 140iterations 2.2824297E-03 4.9011230E-02 at 150iterations 1.2675998E-03 3.1693459E-02 at 160iterations 7.0318300E-04 1.6041756E-02 at 170iterations 3.9142804E-04 7.7657700E-03 at 180iterations finished qdiffx linear iterations at : 11:03:53 total time elapsed so far: 12.33000 # loops : 180 mean,max change (kT/e) : 3.9142804E-04 7.7657700E-03 energy calculations done at 12.33000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.54000 DelPhi exited at 11:03:54 12.539u 0.216s 0:13.19 96.5% 0+0k 0+0io 0pf+0w