Sat Oct 8 12:17:01 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 12:17:01 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 = 3108 !!! WARNING: SEP 172 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6010062 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): -14.59400 44.64000 ymin,ymax (A): -12.60300 45.81900 zmin,zma (A): -5.200000 52.71400 x,y,z range (A): 59.23400 58.42200 57.91400 scale (grids/A): 0.6010062 object centre (A): 15.02300 16.60800 23.75700 number of atom coordinates read : 3108 total number of charged atoms : 2968 net assigned charge : 2.525006 assigned positive charge : 428.8920 centred at (gu) : 89.04280 89.55935 88.55943 assigned negative charge : -426.3682 centred at (gu) : 88.90675 89.71832 88.59241 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7815 nv = 96 ne = 84 npr = 62598 no. pairs analyzed = 62598 no. exposed pairs = 4575 no. arc points = 32286 no. surface atoms = 1537 nbur = 1571 mkacc time = 0.1600000 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 = 1.456000 m= 420 mr = 3544 m= 1 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 4660 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3084 ## 257 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 9424 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.4480845E-09 -1.5533443E-10 midg,1,midg; midg,igrid,midg 8.3685316E-09 -5.0033315E-09 1,midg,midg; igrid,midg,midg -5.7215970E-09 5.3492699E-09 gauss-seidel spectral radius is 0.9857422 estimated iterations to convergence 69 setup time was (sec) 0.6700000 now iterating at: 12:17:02 rms-change max change #iterations 0.1116195 18.44453 at 10iterations 1.0705680E-02 1.548823 at 20iterations 2.5909769E-03 0.4360046 at 30iterations 1.1214813E-03 0.1963005 at 40iterations 5.0918938E-04 8.9477539E-02 at 50iterations finished qdiffx linear iterations at : 12:17:07 total time elapsed so far: 5.070000 # loops : 50 mean,max change (kT/e) : 5.0918938E-04 8.9477539E-02 energy calculations done at 5.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.230000 DelPhi exited at 12:17:07 5.232u 0.480s 0:06.00 95.1% 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 Sat Oct 8 2011 at 12:17:07 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 = 3108 !!! WARNING: SEP 172 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.803018 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): -14.59400 44.64000 ymin,ymax (A): -12.60300 45.81900 zmin,zma (A): -5.200000 52.71400 x,y,z range (A): 59.23400 58.42200 57.91400 scale (grids/A): 1.803018 object centre (A): 15.02300 16.60800 23.75700 number of atom coordinates read : 3108 total number of charged atoms : 2968 net assigned charge : 2.525006 assigned positive charge : 428.8920 centred at (gu) : 87.12716 88.67709 85.67739 assigned negative charge : -426.3682 centred at (gu) : 86.72018 89.15495 85.77689 start vw surface at 0.1300000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 83826 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32286 grid for indexing accessible points = 1.400000 m= 27210 mr = 52508 m= 4047 mr = 17397 m= 209 mr = 2094 m= 3 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7200000 number of dielectric boundary points 43255 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 171 iepsmp to db, and charging done at 0.9100000 number of grid points assigned charge 23202 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) : 0.6010062 object centre at (A) : 15.02300 16.60800 23.75700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.4905306E-03 1.1113230E-02 midg,1,midg; midg,igrid,midg -1.4810310E-03 1.3323055E-03 1,midg,midg; igrid,midg,midg -1.5861519E-02 5.0978731E-02 gauss-seidel spectral radius is 0.9985712 estimated iterations to convergence 210 setup time was (sec) 1.120000 now iterating at: 12:17:09 rms-change max change #iterations 4.040928 185.4756 at 10iterations 1.839795 72.90344 at 20iterations 0.8440272 30.09312 at 30iterations 0.3874442 12.95668 at 40iterations 0.1779586 5.864658 at 50iterations 8.1951186E-02 2.810865 at 60iterations 3.7872177E-02 1.302959 at 70iterations 1.7869877E-02 0.5996628 at 80iterations 8.8284640E-03 0.2848129 at 90iterations 4.7500767E-03 0.1760521 at 100iterations 2.8668246E-03 0.1166458 at 110iterations 1.9619451E-03 7.0890427E-02 at 120iterations finished qdiffx linear iterations at : 12:17:20 total time elapsed so far: 12.59000 # loops : 120 mean,max change (kT/e) : 1.9619451E-03 7.0890427E-02 energy calculations done at 12.59000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.77000 DelPhi exited at 12:17:21 12.774u 0.522s 0:13.62 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 12:17:21 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3108 !!! WARNING: SEP 172 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.704528 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): -14.59400 44.64000 ymin,ymax (A): -12.60300 45.81900 zmin,zma (A): -5.200000 52.71400 x,y,z range (A): 59.23400 58.42200 57.91400 scale (grids/A): 2.704528 object centre (A): 15.02300 16.60800 23.75700 number of atom coordinates read : 3108 total number of charged atoms : 2968 net assigned charge : 2.525006 assigned positive charge : 428.8920 centred at (gu) : 85.69069 88.01537 83.51589 assigned negative charge : -426.3682 centred at (gu) : 85.08015 88.73235 83.66509 start vw surface at 0.1400000 fill in re-entrant regions at 0.6700000 boundary points on vw surface= 194036 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32286 grid for indexing accessible points = 1.400000 m= 88317 mr = 129776 m= 30317 mr = 66267 m= 6871 mr = 21855 m= 806 mr = 4527 m= 32 mr = 387 m= 0 mr = 1 time to grow re-entrant surface = 1.130000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.940000 number of dielectric boundary points 97566 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 2.110000 number of grid points assigned charge 23742 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) : 1.803018 object centre at (A) : 15.02300 16.60800 23.75700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.1384741E-02 0.1178403 midg,1,midg; midg,igrid,midg -0.1265750 -2.8600296E-02 1,midg,midg; igrid,midg,midg -0.5788168 0.6992690 gauss-seidel spectral radius is 0.9992783 estimated iterations to convergence 294 setup time was (sec) 2.360000 now iterating at: 12:17:24 rms-change max change #iterations 10.08248 311.9380 at 10iterations 6.127632 162.3210 at 20iterations 3.686981 86.35075 at 30iterations 2.195836 60.84296 at 40iterations 1.300813 26.03739 at 50iterations 0.7680699 15.24657 at 60iterations 0.4514890 9.921808 at 70iterations 0.2648132 5.540244 at 80iterations 0.1547790 2.899940 at 90iterations 9.0517305E-02 1.744850 at 100iterations 5.2953787E-02 0.9738064 at 110iterations 3.0914012E-02 0.6411476 at 120iterations 1.8156368E-02 0.3096905 at 130iterations 1.0732216E-02 0.2271121 at 140iterations 6.4649247E-03 0.1363869 at 150iterations 4.0238397E-03 7.6541901E-02 at 160iterations 2.6440176E-03 5.6327820E-02 at 170iterations 1.8682878E-03 4.0500641E-02 at 180iterations finished qdiffx linear iterations at : 12:17:44 total time elapsed so far: 22.44000 # loops : 180 mean,max change (kT/e) : 1.8682878E-03 4.0500641E-02 energy calculations done at 22.44000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 22.62000 DelPhi exited at 12:17:45 22.624u 0.552s 0:23.62 98.0% 0+0k 0+0io 0pf+0w