Mon Oct 10 19:33:23 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+sph.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 = amb.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 Mon Oct 10 2011 at 19:33:23 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3041 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: 0.6016257 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): -11.37800 45.51700 ymin,ymax (A): -17.91000 39.72200 zmin,zma (A): -12.86600 46.30700 x,y,z range (A): 56.89500 57.63200 59.17300 scale (grids/A): 0.6016257 object centre (A): 17.06950 10.90600 16.72050 number of atom coordinates read : 3041 total number of charged atoms : 2900 net assigned charge : -1.499975 assigned positive charge : 457.3360 centred at (gu) : 88.75549 89.30545 90.50477 assigned negative charge : -458.8374 centred at (gu) : 88.77154 89.27628 90.53008 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7288 nv = 96 ne = 84 npr = 60891 no. pairs analyzed = 60891 no. exposed pairs = 4216 no. arc points = 29675 no. surface atoms = 1409 nbur = 1632 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= 369 mr = 3544 m= 2 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 4084 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2928 ## 272 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 9077 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.1733411E-10 -2.0392998E-09 midg,1,midg; midg,igrid,midg -2.3364868E-09 5.4662919E-10 1,midg,midg; igrid,midg,midg 8.7447750E-11 -1.0581205E-09 gauss-seidel spectral radius is 0.9857472 estimated iterations to convergence 69 setup time was (sec) 0.6700000 now iterating at: 19:33:24 rms-change max change #iterations 0.1174158 24.69663 at 10iterations 1.0009694E-02 1.501036 at 20iterations 9.5697021E-04 0.1746511 at 30iterations 1.6712445E-04 3.2485962E-02 at 40iterations 5.3420157E-05 1.0534286E-02 at 50iterations finished qdiffx linear iterations at : 19:33:29 total time elapsed so far: 5.000000 # loops : 50 mean,max change (kT/e) : 5.3420157E-05 1.0534286E-02 energy calculations done at 5.000000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.170000 DelPhi exited at 19:33:30 5.179u 0.481s 0:06.40 88.2% 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 Mon Oct 10 2011 at 19:33:30 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3041 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: 1.804877 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): -11.37800 45.51700 ymin,ymax (A): -17.91000 39.72200 zmin,zma (A): -12.86600 46.30700 x,y,z range (A): 56.89500 57.63200 59.17300 scale (grids/A): 1.804877 object centre (A): 17.06950 10.90600 16.72050 number of atom coordinates read : 3041 total number of charged atoms : 2900 net assigned charge : -1.499975 assigned positive charge : 457.3360 centred at (gu) : 86.26573 87.91512 91.51340 assigned negative charge : -458.8374 centred at (gu) : 86.31433 87.82850 91.58994 start vw surface at 0.1300000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 78508 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29675 grid for indexing accessible points = 1.400000 m= 26241 mr = 50920 m= 3781 mr = 17815 m= 148 mr = 2080 m= 0 mr = 16 time to grow re-entrant surface = 0.4200000 no. cavity mid-points inaccessible to solvent = 28 time to turn everything in is 0.7900000 number of dielectric boundary points 37847 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 179 iepsmp to db, and charging done at 1.000000 number of grid points assigned charge 22636 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) : 0.6016257 object centre at (A) : 17.06950 10.90600 16.72050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.3312393E-03 -2.3630790E-02 midg,1,midg; midg,igrid,midg 7.8584468E-03 1.8386422E-02 1,midg,midg; igrid,midg,midg 5.8294320E-03 -3.5573398E-03 gauss-seidel spectral radius is 0.9985430 estimated iterations to convergence 208 setup time was (sec) 1.330000 now iterating at: 19:33:32 rms-change max change #iterations 4.256083 172.7265 at 10iterations 1.928894 72.91179 at 20iterations 0.8777487 32.27124 at 30iterations 0.4011732 12.47551 at 40iterations 0.1825346 6.275213 at 50iterations 8.3290100E-02 2.609955 at 60iterations 3.7981901E-02 1.295654 at 70iterations 1.7340422E-02 0.5101204 at 80iterations 7.9193711E-03 0.2667699 at 90iterations 3.6238334E-03 0.1243372 at 100iterations 1.6799304E-03 5.1380157E-02 at 110iterations 7.8436913E-04 2.5695801E-02 at 120iterations finished qdiffx linear iterations at : 19:33:50 total time elapsed so far: 18.99000 # loops : 120 mean,max change (kT/e) : 7.8436913E-04 2.5695801E-02 energy calculations done at 18.99000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.22000 DelPhi exited at 19:33:50 19.226u 0.913s 0:20.52 98.0% 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 Mon Oct 10 2011 at 19:33:50 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3041 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: 2.707316 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): -11.37800 45.51700 ymin,ymax (A): -17.91000 39.72200 zmin,zma (A): -12.86600 46.30700 x,y,z range (A): 56.89500 57.63200 59.17300 scale (grids/A): 2.707316 object centre (A): 17.06950 10.90600 16.72050 number of atom coordinates read : 3041 total number of charged atoms : 2900 net assigned charge : -1.499975 assigned positive charge : 457.3360 centred at (gu) : 84.39855 86.87266 92.26994 assigned negative charge : -458.8374 centred at (gu) : 84.47144 86.74269 92.38493 start vw surface at 0.1400000 fill in re-entrant regions at 0.6200000 boundary points on vw surface= 181759 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29675 grid for indexing accessible points = 1.400000 m= 85242 mr = 125249 m= 29327 mr = 66122 m= 6473 mr = 21969 m= 688 mr = 4406 m= 19 mr = 351 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 1.220000 no. cavity mid-points inaccessible to solvent = 60 time to turn everything in is 2.050000 number of dielectric boundary points 85408 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.350000 number of grid points assigned charge 23192 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) : 1.804877 object centre at (A) : 17.06950 10.90600 16.72050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.7028090E-02 -0.2826992 midg,1,midg; midg,igrid,midg 0.1431011 0.3467302 1,midg,midg; igrid,midg,midg 0.1385675 -6.2459305E-02 gauss-seidel spectral radius is 0.9992549 estimated iterations to convergence 289 setup time was (sec) 2.710000 now iterating at: 19:33:54 rms-change max change #iterations 10.32401 341.5715 at 10iterations 6.108640 139.7574 at 20iterations 3.573829 79.72997 at 30iterations 2.078219 43.53997 at 40iterations 1.208111 26.12917 at 50iterations 0.7006032 13.88002 at 60iterations 0.4042386 7.811400 at 70iterations 0.2331523 4.429359 at 80iterations 0.1346058 2.560606 at 90iterations 7.7486359E-02 1.510949 at 100iterations 4.4672213E-02 0.8294897 at 110iterations 2.5724931E-02 0.4612162 at 120iterations 1.4782253E-02 0.2679234 at 130iterations 8.5429735E-03 0.1585488 at 140iterations 4.9328664E-03 9.7009659E-02 at 150iterations 2.8676309E-03 5.0398350E-02 at 160iterations 1.6895353E-03 3.1265259E-02 at 170iterations 1.0171056E-03 2.1070004E-02 at 180iterations finished qdiffx linear iterations at : 19:34:24 total time elapsed so far: 32.95000 # loops : 180 mean,max change (kT/e) : 1.0171056E-03 2.1070004E-02 energy calculations done at 32.95000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 33.12000 DelPhi exited at 19:34:25 33.121u 0.912s 0:34.67 98.1% 0+0k 0+0io 0pf+0w