Tue Jan 24 12:18:57 PST 2012 #!/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 Tue Jan 24 2012 at 12:18:58 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: 936 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5496 !!! WARNING: ZN1 990 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.5287312 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): -18.85600 48.47500 ymin,ymax (A): -58.39800 6.901000 zmin,zma (A): -29.95400 32.85400 x,y,z range (A): 67.33100 65.29900 62.80800 scale (grids/A): 0.5287312 object centre (A): 14.80950 -25.74850 1.450000 number of atom coordinates read : 5496 total number of charged atoms : 5324 net assigned charge : -10.60001 assigned positive charge : 844.5702 centred at (gu) : 89.63299 90.12318 91.51485 assigned negative charge : -855.1769 centred at (gu) : 89.70992 90.12177 91.52689 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 9576 nv = 96 ne = 84 npr = 112421 no. pairs analyzed = 112421 no. exposed pairs = 6447 no. arc points = 44708 no. surface atoms = 2159 nbur = 3337 mkacc time = 0.2300000 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 = 1.596000 m= 339 mr = 5263 m= 1 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 22 time to turn everything in is 0.4300000 number of dielectric boundary points 4639 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4340 ## 585 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 12839 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.7330810E-10 -5.9736754E-10 midg,1,midg; midg,igrid,midg -3.2777003E-10 -3.2942968E-10 1,midg,midg; igrid,midg,midg 1.8883931E-10 -7.6317219E-10 gauss-seidel spectral radius is 0.9817453 estimated iterations to convergence 61 setup time was (sec) 0.6300000 now iterating at: 12:19:00 rms-change max change #iterations 8.3927475E-02 11.20676 at 10iterations 5.3421925E-03 0.8189812 at 20iterations 4.0534310E-04 4.8797607E-02 at 30iterations 6.1688654E-05 7.8506470E-03 at 40iterations 1.4804686E-05 1.8739700E-03 at 50iterations finished qdiffx linear iterations at : 12:19:03 total time elapsed so far: 3.590000 # loops : 50 mean,max change (kT/e) : 1.4804686E-05 1.8739700E-03 energy calculations done at 3.590000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.730000 DelPhi exited at 12:19:03 3.739u 0.202s 0:04.78 82.2% 0+0k 0+46792io 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 Tue Jan 24 2012 at 12:19:03 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: 936 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5496 !!! WARNING: ZN1 990 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.586194 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): -18.85600 48.47500 ymin,ymax (A): -58.39800 6.901000 zmin,zma (A): -29.95400 32.85400 x,y,z range (A): 67.33100 65.29900 62.80800 scale (grids/A): 1.586194 object centre (A): 14.80950 -25.74850 1.450000 number of atom coordinates read : 5496 total number of charged atoms : 5324 net assigned charge : -10.60001 assigned positive charge : 844.5702 centred at (gu) : 88.89735 90.36765 94.54298 assigned negative charge : -855.1769 centred at (gu) : 89.12975 90.36486 94.58053 start vw surface at 0.1700000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 109417 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44708 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 32937 mr = 77989 m= 3191 mr = 22801 m= 97 mr = 1472 m= 0 mr = 6 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 2752 time to turn everything in is 0.6400000 number of dielectric boundary points 43374 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 487 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 40348 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) : 0.5287312 object centre at (A) : 14.80950 -25.74850 1.450000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.8072236E-02 -1.9884426E-02 midg,1,midg; midg,igrid,midg -1.3650987E-02 -2.2142433E-02 1,midg,midg; igrid,midg,midg 3.2806851E-03 -8.4496988E-03 gauss-seidel spectral radius is 0.9983060 estimated iterations to convergence 193 setup time was (sec) 0.8600000 now iterating at: 12:19:04 rms-change max change #iterations 4.525849 170.9457 at 10iterations 1.947752 73.92953 at 20iterations 0.8355669 24.44809 at 30iterations 0.3588619 10.57621 at 40iterations 0.1544167 4.373089 at 50iterations 6.6906147E-02 1.873621 at 60iterations 2.8662911E-02 0.8843048 at 70iterations 1.2352427E-02 0.3568964 at 80iterations 5.3253430E-03 0.1483536 at 90iterations 2.2977837E-03 7.4890137E-02 at 100iterations 9.9025026E-04 2.8650284E-02 at 110iterations 4.2837474E-04 1.1962891E-02 at 120iterations finished qdiffx linear iterations at : 12:19:12 total time elapsed so far: 8.170000 # loops : 120 mean,max change (kT/e) : 4.2837474E-04 1.1962891E-02 energy calculations done at 8.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.320000 DelPhi exited at 12:19:12 8.326u 0.208s 0:09.47 89.9% 0+0k 0+45704io 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 Tue Jan 24 2012 at 12:19:13 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: 936 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5496 !!! WARNING: ZN1 990 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.379290 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): -18.85600 48.47500 ymin,ymax (A): -58.39800 6.901000 zmin,zma (A): -29.95400 32.85400 x,y,z range (A): 67.33100 65.29900 62.80800 scale (grids/A): 2.379290 object centre (A): 14.80950 -25.74850 1.450000 number of atom coordinates read : 5496 total number of charged atoms : 5324 net assigned charge : -10.60001 assigned positive charge : 844.5702 centred at (gu) : 88.34577 90.55129 96.81423 assigned negative charge : -855.1769 centred at (gu) : 88.69469 90.54723 96.87064 start vw surface at 0.1700000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 255588 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44708 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 116365 mr = 190823 m= 31171 mr = 93051 m= 4915 mr = 23329 m= 319 mr = 3154 m= 6 mr = 102 m= 0 mr = 0 time to grow re-entrant surface = 1.030000 no. cavity mid-points inaccessible to solvent = 9144 time to turn everything in is 1.610000 number of dielectric boundary points 97905 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 49 iepsmp to db, and charging done at 1.720000 number of grid points assigned charge 42528 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) : 1.586194 object centre at (A) : 14.80950 -25.74850 1.450000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3380519 -0.2507289 midg,1,midg; midg,igrid,midg -0.1352152 -0.4154326 1,midg,midg; igrid,midg,midg 0.1283966 3.7241209E-02 gauss-seidel spectral radius is 0.9992231 estimated iterations to convergence 283 setup time was (sec) 1.860000 now iterating at: 12:19:16 rms-change max change #iterations 11.87620 271.9034 at 10iterations 6.922423 144.6730 at 20iterations 3.987506 76.12721 at 30iterations 2.292986 40.18741 at 40iterations 1.312742 22.10124 at 50iterations 0.7504004 13.12301 at 60iterations 0.4281217 7.387207 at 70iterations 0.2436262 4.197840 at 80iterations 0.1388029 2.275337 at 90iterations 7.8744024E-02 1.305906 at 100iterations 4.4770975E-02 0.7573547 at 110iterations 2.5389139E-02 0.4046898 at 120iterations 1.4434469E-02 0.2479272 at 130iterations 8.1906049E-03 0.1401711 at 140iterations 4.6480680E-03 7.6967150E-02 at 150iterations 2.6341886E-03 4.3518066E-02 at 160iterations 1.4958428E-03 2.6239395E-02 at 170iterations 8.4946328E-04 1.4302254E-02 at 180iterations finished qdiffx linear iterations at : 12:19:27 total time elapsed so far: 13.63000 # loops : 180 mean,max change (kT/e) : 8.4946328E-04 1.4302254E-02 energy calculations done at 13.63000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.77000 DelPhi exited at 12:19:28 13.778u 0.230s 0:15.35 91.2% 0+0k 0+45696io 0pf+0w