Sat Oct 15 12:34:10 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 15 2011 at 12:34:10 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: 260 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1650 !!! WARNING: MN4 436 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7530088 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): 6.383000 51.14300 ymin,ymax (A): 15.49100 62.76800 zmin,zma (A): -8.665000 36.63300 x,y,z range (A): 44.76000 47.27700 45.29800 scale (grids/A): 0.7530088 object centre (A): 28.76300 39.12950 13.98400 number of atom coordinates read : 1650 total number of charged atoms : 1513 net assigned charge : -8.099994 assigned positive charge : 242.6202 centred at (gu) : 90.21786 88.61069 89.64556 assigned negative charge : -250.7201 centred at (gu) : 90.27232 88.28320 90.12316 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6362 nv = 96 ne = 84 npr = 35498 no. pairs analyzed = 35498 no. exposed pairs = 2084 no. arc points = 14692 no. surface atoms = 711 nbur = 939 mkacc time = 8.0000006E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 452 mr = 3554 m= 2 mr = 89 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 47 time to turn everything in is 0.2100000 number of dielectric boundary points 3173 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1128 ## 70 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 6528 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.0861688E-07 -6.5311082E-07 midg,1,midg; midg,igrid,midg -6.8791365E-07 1.0912718E-07 1,midg,midg; igrid,midg,midg -1.2217853E-07 -2.4857010E-07 gauss-seidel spectral radius is 0.9907587 estimated iterations to convergence 84 setup time was (sec) 0.5000000 now iterating at: 12:34:11 rms-change max change #iterations 0.2336337 76.92047 at 10iterations 3.2074716E-02 7.407928 at 20iterations 4.4380832E-03 0.7249756 at 30iterations 6.1646826E-04 8.3848000E-02 at 40iterations 8.5857173E-05 1.2905121E-02 at 50iterations finished qdiffx linear iterations at : 12:34:15 total time elapsed so far: 4.990000 # loops : 50 mean,max change (kT/e) : 8.5857173E-05 1.2905121E-02 energy calculations done at 4.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.160000 DelPhi exited at 12:34:16 5.160u 0.497s 0:06.13 92.1% 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 15 2011 at 12:34:16 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: 260 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1650 !!! WARNING: MN4 436 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.259027 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): 6.383000 51.14300 ymin,ymax (A): 15.49100 62.76800 zmin,zma (A): -8.665000 36.63300 x,y,z range (A): 44.76000 47.27700 45.29800 scale (grids/A): 2.259027 object centre (A): 28.76300 39.12950 13.98400 number of atom coordinates read : 1650 total number of charged atoms : 1513 net assigned charge : -8.099994 assigned positive charge : 242.6202 centred at (gu) : 90.65382 85.83200 88.93687 assigned negative charge : -250.7201 centred at (gu) : 90.81692 84.84956 90.36967 start vw surface at 0.1000000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 66358 reading accessible surface arcs data from file ARCDAT no. of arc points read = 14692 grid for indexing accessible points = 1.400000 m= 26738 mr = 45415 m= 5513 mr = 20791 m= 513 mr = 3876 m= 12 mr = 277 m= 0 mr = 3 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 1138 time to turn everything in is 0.6100000 number of dielectric boundary points 28772 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 28 iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 12066 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) : 0.7530088 object centre at (A) : 28.76300 39.12950 13.98400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.3428415E-02 -0.1087147 midg,1,midg; midg,igrid,midg -0.1006265 3.3288930E-02 1,midg,midg; igrid,midg,midg -6.0997605E-02 -6.5671243E-02 gauss-seidel spectral radius is 0.9989119 estimated iterations to convergence 240 setup time was (sec) 0.9800000 now iterating at: 12:34:17 rms-change max change #iterations 4.610170 247.9770 at 10iterations 2.336362 141.0330 at 20iterations 1.178306 43.20431 at 30iterations 0.6019781 24.21973 at 40iterations 0.3051023 9.518650 at 50iterations 0.1552148 4.966268 at 60iterations 7.8566246E-02 2.373988 at 70iterations 4.0003121E-02 1.271352 at 80iterations 2.0233503E-02 0.6627998 at 90iterations 1.0277459E-02 0.2964554 at 100iterations 5.2196640E-03 0.1626129 at 110iterations 2.6523385E-03 8.0699921E-02 at 120iterations finished qdiffx linear iterations at : 12:34:29 total time elapsed so far: 12.64000 # loops : 120 mean,max change (kT/e) : 2.6523385E-03 8.0699921E-02 energy calculations done at 12.64000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.81000 DelPhi exited at 12:34:30 12.812u 0.507s 0:13.88 95.8% 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 15 2011 at 12:34:30 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: 260 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1650 !!! WARNING: MN4 436 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.388540 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): 6.383000 51.14300 ymin,ymax (A): 15.49100 62.76800 zmin,zma (A): -8.665000 36.63300 x,y,z range (A): 44.76000 47.27700 45.29800 scale (grids/A): 3.388540 object centre (A): 28.76300 39.12950 13.98400 number of atom coordinates read : 1650 total number of charged atoms : 1513 net assigned charge : -8.099994 assigned positive charge : 242.6202 centred at (gu) : 90.98069 83.74803 88.40530 assigned negative charge : -250.7201 centred at (gu) : 91.22536 82.27440 90.55454 start vw surface at 0.1000000 fill in re-entrant regions at 0.7500000 boundary points on vw surface= 152639 reading accessible surface arcs data from file ARCDAT no. of arc points read = 14692 grid for indexing accessible points = 1.400000 m= 81589 mr = 109334 m= 35469 mr = 68256 m= 10523 mr = 29948 m= 2121 mr = 8394 m= 283 mr = 1619 m= 22 mr = 211 m= 0 mr = 15 time to grow re-entrant surface = 0.9499999 no. cavity mid-points inaccessible to solvent = 3983 time to turn everything in is 1.850000 number of dielectric boundary points 64869 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.010000 number of grid points assigned charge 12104 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) : 2.259027 object centre at (A) : 28.76300 39.12950 13.98400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4736809 -0.6875269 midg,1,midg; midg,igrid,midg -0.9045638 0.3373553 1,midg,midg; igrid,midg,midg -0.3679340 -0.4611174 gauss-seidel spectral radius is 0.9993119 estimated iterations to convergence 301 setup time was (sec) 2.240000 now iterating at: 12:34:33 rms-change max change #iterations 9.856281 617.4471 at 10iterations 5.767548 145.4663 at 20iterations 3.372053 76.91058 at 30iterations 1.976782 55.00831 at 40iterations 1.153699 20.23235 at 50iterations 0.6751641 14.59131 at 60iterations 0.3953516 6.686843 at 70iterations 0.2314821 4.266084 at 80iterations 0.1350488 2.276844 at 90iterations 7.9281785E-02 1.329577 at 100iterations 4.6350785E-02 0.8320428 at 110iterations 2.7152011E-02 0.4549742 at 120iterations 1.5862100E-02 0.3052397 at 130iterations 9.2784930E-03 0.1733112 at 140iterations 5.4245531E-03 9.1554642E-02 at 150iterations 3.1831556E-03 5.5157661E-02 at 160iterations 1.8627150E-03 3.6144972E-02 at 170iterations 1.0873567E-03 1.9998550E-02 at 180iterations finished qdiffx linear iterations at : 12:34:52 total time elapsed so far: 21.44000 # loops : 180 mean,max change (kT/e) : 1.0873567E-03 1.9998550E-02 energy calculations done at 21.44000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.62000 DelPhi exited at 12:34:52 21.620u 0.540s 0:22.45 98.7% 0+0k 0+0io 0pf+0w