Fri Nov 11 22:54:54 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+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 Fri Nov 11 2011 at 22:54:54 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 ! Automatically converted by prot2crg.py # of charge parameter records: 929 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2635 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: 0.6003271 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): -10.32600 37.36200 ymin,ymax (A): 9.7000003E-02 59.39800 zmin,zma (A): -24.04700 27.93800 x,y,z range (A): 47.68800 59.30100 51.98500 scale (grids/A): 0.6003271 object centre (A): 13.51800 29.74750 1.945500 number of atom coordinates read : 2635 total number of charged atoms : 2499 net assigned charge : 9.500011 assigned positive charge : 388.4413 centred at (gu) : 90.02304 88.77753 89.74783 assigned negative charge : -378.9426 centred at (gu) : 90.11539 88.70034 89.80337 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 6488 nv = 96 ne = 84 npr = 51563 no. pairs analyzed = 51563 no. exposed pairs = 3663 no. arc points = 25562 no. surface atoms = 1214 nbur = 1421 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 300 mr = 3279 m= 3 mr = 22 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 13 time to turn everything in is 0.2400000 number of dielectric boundary points 3490 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2518 ## 256 charges are in solution ## iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 7901 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.4834520E-09 2.0260909E-09 midg,1,midg; midg,igrid,midg 1.7087589E-09 5.2525042E-09 1,midg,midg; igrid,midg,midg 7.3904665E-09 7.9247725E-10 gauss-seidel spectral radius is 0.9856506 estimated iterations to convergence 68 setup time was (sec) 0.4400000 now iterating at: 22:54:54 rms-change max change #iterations 0.1058646 16.30454 at 10iterations 9.0286350E-03 1.431332 at 20iterations 7.7457144E-04 0.1153736 at 30iterations 9.2442388E-05 1.6077042E-02 at 40iterations 3.0038538E-05 4.6243668E-03 at 50iterations finished qdiffx linear iterations at : 22:54:57 total time elapsed so far: 3.390000 # loops : 50 mean,max change (kT/e) : 3.0038538E-05 4.6243668E-03 energy calculations done at 3.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.530000 DelPhi exited at 22:54:58 3.539u 0.177s 0:04.14 89.3% 0+0k 0+45872io 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 Fri Nov 11 2011 at 22:54:58 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 ! Automatically converted by prot2crg.py # of charge parameter records: 929 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2635 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: 1.800981 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): -10.32600 37.36200 ymin,ymax (A): 9.7000003E-02 59.39800 zmin,zma (A): -24.04700 27.93800 x,y,z range (A): 47.68800 59.30100 51.98500 scale (grids/A): 1.800981 object centre (A): 13.51800 29.74750 1.945500 number of atom coordinates read : 2635 total number of charged atoms : 2499 net assigned charge : 9.500011 assigned positive charge : 388.4413 centred at (gu) : 90.06830 86.33210 89.24284 assigned negative charge : -378.9426 centred at (gu) : 90.34591 86.10072 89.40977 start vw surface at 0.1100000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 70204 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25562 grid for indexing accessible points = 1.400000 m= 24016 mr = 46801 m= 3347 mr = 16758 m= 140 mr = 1843 m= 2 mr = 35 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 1376 time to turn everything in is 0.4400000 number of dielectric boundary points 32272 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 165 iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 19333 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) : 0.6003271 object centre at (A) : 13.51800 29.74750 1.945500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.7850995E-02 -4.4976878E-03 midg,1,midg; midg,igrid,midg -5.5934157E-04 1.8911390E-02 1,midg,midg; igrid,midg,midg 2.2219542E-02 4.3325229E-03 gauss-seidel spectral radius is 0.9984961 estimated iterations to convergence 205 setup time was (sec) 0.6500000 now iterating at: 22:54:59 rms-change max change #iterations 3.789227 209.3108 at 10iterations 1.710397 64.43404 at 20iterations 0.7730401 26.82617 at 30iterations 0.3483287 11.67477 at 40iterations 0.1573537 5.351896 at 50iterations 7.1361721E-02 2.413982 at 60iterations 3.2223281E-02 1.046183 at 70iterations 1.4531450E-02 0.5282734 at 80iterations 6.5604299E-03 0.2656250 at 90iterations 2.9708773E-03 8.7234497E-02 at 100iterations 1.3405279E-03 4.7428131E-02 at 110iterations 6.0815807E-04 2.1293640E-02 at 120iterations finished qdiffx linear iterations at : 22:55:06 total time elapsed so far: 7.880000 # loops : 120 mean,max change (kT/e) : 6.0815807E-04 2.1293640E-02 energy calculations done at 7.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.020000 DelPhi exited at 22:55:06 8.026u 0.207s 0:08.54 96.2% 0+0k 0+45256io 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 Fri Nov 11 2011 at 22:55:07 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 ! Automatically converted by prot2crg.py # of charge parameter records: 929 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2635 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: 2.701472 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): -10.32600 37.36200 ymin,ymax (A): 9.7000003E-02 59.39800 zmin,zma (A): -24.04700 27.93800 x,y,z range (A): 47.68800 59.30100 51.98500 scale (grids/A): 2.701472 object centre (A): 13.51800 29.74750 1.945500 number of atom coordinates read : 2635 total number of charged atoms : 2499 net assigned charge : 9.500011 assigned positive charge : 388.4413 centred at (gu) : 90.10217 84.49794 88.86391 assigned negative charge : -378.9426 centred at (gu) : 90.51878 84.15103 89.11473 start vw surface at 0.1100000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 162356 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25562 grid for indexing accessible points = 1.400000 m= 78636 mr = 114343 m= 26724 mr = 62098 m= 5680 mr = 20544 m= 575 mr = 3917 m= 26 mr = 319 m= 0 mr = 2 time to grow re-entrant surface = 0.7400000 no. cavity mid-points inaccessible to solvent = 4776 time to turn everything in is 1.150000 number of dielectric boundary points 72774 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.240000 number of grid points assigned charge 19960 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) : 1.800981 object centre at (A) : 13.51800 29.74750 1.945500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4066685 -1.8349150E-02 midg,1,midg; midg,igrid,midg -0.1313510 0.1503457 1,midg,midg; igrid,midg,midg 0.2291884 5.1453147E-02 gauss-seidel spectral radius is 0.9992305 estimated iterations to convergence 285 setup time was (sec) 1.380000 now iterating at: 22:55:08 rms-change max change #iterations 9.165688 326.3652 at 10iterations 5.342108 142.7432 at 20iterations 3.091638 70.13786 at 30iterations 1.782057 42.11095 at 40iterations 1.024279 21.46567 at 50iterations 0.5880535 11.56061 at 60iterations 0.3357729 7.162725 at 70iterations 0.1917130 3.834599 at 80iterations 0.1094915 2.086662 at 90iterations 6.2432297E-02 1.228334 at 100iterations 3.5624031E-02 0.7295732 at 110iterations 2.0262860E-02 0.3862348 at 120iterations 1.1574759E-02 0.2184734 at 130iterations 6.5916204E-03 0.1531172 at 140iterations 3.7382846E-03 7.2441101E-02 at 150iterations 2.1308409E-03 4.2449951E-02 at 160iterations 1.2140459E-03 2.2804260E-02 at 170iterations 6.9278548E-04 1.3732910E-02 at 180iterations finished qdiffx linear iterations at : 22:55:20 total time elapsed so far: 12.82000 # loops : 180 mean,max change (kT/e) : 6.9278548E-04 1.3732910E-02 energy calculations done at 12.82000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.96000 DelPhi exited at 22:55:20 12.966u 0.228s 0:13.56 97.1% 0+0k 0+45248io 0pf+0w