Sat Oct 8 17:08:34 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 Sat Oct 8 2011 at 17:08:34 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3482 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: 0.5188673 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): -14.18100 44.44600 ymin,ymax (A): -39.43100 29.18000 zmin,zma (A): -16.82800 35.41100 x,y,z range (A): 58.62700 68.61100 52.23901 scale (grids/A): 0.5188673 object centre (A): 15.13250 -5.125500 9.291501 number of atom coordinates read : 3482 total number of charged atoms : 3336 net assigned charge : -4.499981 assigned positive charge : 523.9742 centred at (gu) : 90.46523 92.14880 90.58429 assigned negative charge : -528.4758 centred at (gu) : 90.48255 92.14980 90.53275 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 5902 nv = 96 ne = 84 npr = 70979 no. pairs analyzed = 70979 no. exposed pairs = 4333 no. arc points = 30181 no. surface atoms = 1459 nbur = 2023 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 = 1.680000 m= 205 mr = 3059 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4900000 number of dielectric boundary points 3041 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3004 ## 461 charges are in solution ## iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 7967 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.9947834E-10 5.4882644E-11 midg,1,midg; midg,igrid,midg -5.2249614E-11 -1.6376772E-10 1,midg,midg; igrid,midg,midg -4.0410935E-11 -1.5631647E-10 gauss-seidel spectral radius is 0.9809052 estimated iterations to convergence 60 setup time was (sec) 0.8300000 now iterating at: 17:08:36 rms-change max change #iterations 5.9845675E-02 10.87222 at 10iterations 3.6614076E-03 0.5442200 at 20iterations 3.6363030E-04 6.4471722E-02 at 30iterations 8.3300918E-05 1.5807152E-02 at 40iterations 2.2808421E-05 4.3430328E-03 at 50iterations finished qdiffx linear iterations at : 17:08:39 total time elapsed so far: 4.500000 # loops : 50 mean,max change (kT/e) : 2.2808421E-05 4.3430328E-03 energy calculations done at 4.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.720000 DelPhi exited at 17:08:40 4.725u 0.430s 0:05.44 94.6% 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 17:08:40 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3482 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: 1.556602 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): -14.18100 44.44600 ymin,ymax (A): -39.43100 29.18000 zmin,zma (A): -16.82800 35.41100 x,y,z range (A): 58.62700 68.61100 52.23901 scale (grids/A): 1.556602 object centre (A): 15.13250 -5.125500 9.291501 number of atom coordinates read : 3482 total number of charged atoms : 3336 net assigned charge : -4.499981 assigned positive charge : 523.9742 centred at (gu) : 91.39449 96.44556 91.75214 assigned negative charge : -528.4758 centred at (gu) : 91.44726 96.44919 91.59784 start vw surface at 0.2000000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 66970 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30181 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 19905 mr = 46152 m= 1711 mr = 13401 m= 31 mr = 745 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 392 time to turn everything in is 0.7200000 number of dielectric boundary points 28319 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 465 ## 7 charges are in solution ## iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 25233 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) : 0.5188673 object centre at (A) : 15.13250 -5.125500 9.291501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.2654531E-03 2.4308141E-03 midg,1,midg; midg,igrid,midg 9.9693369E-03 1.1164409E-03 1,midg,midg; igrid,midg,midg -3.4807546E-03 -1.1373882E-02 gauss-seidel spectral radius is 0.9980368 estimated iterations to convergence 179 setup time was (sec) 1.070000 now iterating at: 17:08:41 rms-change max change #iterations 3.251824 147.5049 at 10iterations 1.311810 50.26947 at 20iterations 0.5285777 20.93805 at 30iterations 0.2135871 8.556053 at 40iterations 8.6146533E-02 2.975473 at 50iterations 3.4701928E-02 1.303355 at 60iterations 1.3941261E-02 0.4955330 at 70iterations 5.6593968E-03 0.1979465 at 80iterations 2.2895101E-03 8.0848694E-02 at 90iterations 9.3629339E-04 3.5398483E-02 at 100iterations 3.8594360E-04 1.4449596E-02 at 110iterations 1.6437327E-04 5.8298111E-03 at 120iterations finished qdiffx linear iterations at : 17:08:53 total time elapsed so far: 12.58000 # loops : 120 mean,max change (kT/e) : 1.6437327E-04 5.8298111E-03 energy calculations done at 12.58000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.81000 DelPhi exited at 17:08:53 12.812u 0.463s 0:13.51 98.2% 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 Sat Oct 8 2011 at 17:08:53 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3482 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: 2.334903 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): -14.18100 44.44600 ymin,ymax (A): -39.43100 29.18000 zmin,zma (A): -16.82800 35.41100 x,y,z range (A): 58.62700 68.61100 52.23901 scale (grids/A): 2.334903 object centre (A): 15.13250 -5.125500 9.291501 number of atom coordinates read : 3482 total number of charged atoms : 3336 net assigned charge : -4.499981 assigned positive charge : 523.9742 centred at (gu) : 92.09146 99.66816 92.62804 assigned negative charge : -528.4758 centred at (gu) : 92.17074 99.67371 92.39671 start vw surface at 0.1700000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 155924 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30181 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 70850 mr = 112904 m= 18159 mr = 55821 m= 2528 mr = 13275 m= 150 mr = 1581 m= 0 mr = 42 time to grow re-entrant surface = 1.030000 no. cavity mid-points inaccessible to solvent = 1252 time to turn everything in is 1.700000 number of dielectric boundary points 63988 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 56 iepsmp to db, and charging done at 1.840000 number of grid points assigned charge 26634 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) : 1.556602 object centre at (A) : 15.13250 -5.125500 9.291501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1097826 4.2949639E-02 midg,1,midg; midg,igrid,midg 0.4016431 7.5641862E-04 1,midg,midg; igrid,midg,midg -4.2338438E-02 -0.1538895 gauss-seidel spectral radius is 0.9990966 estimated iterations to convergence 263 setup time was (sec) 2.070000 now iterating at: 17:08:56 rms-change max change #iterations 8.605908 249.4941 at 10iterations 4.754769 114.9802 at 20iterations 2.607722 59.17079 at 30iterations 1.426525 39.17851 at 40iterations 0.7779772 19.46643 at 50iterations 0.4235377 10.49476 at 60iterations 0.2302072 4.914226 at 70iterations 0.1250073 2.508508 at 80iterations 6.8092853E-02 1.351112 at 90iterations 3.6857169E-02 0.8439064 at 100iterations 1.9953944E-02 0.4144869 at 110iterations 1.0844666E-02 0.2170143 at 120iterations 5.8869924E-03 0.1300325 at 130iterations 3.1977759E-03 7.0329666E-02 at 140iterations 1.7332743E-03 3.8238525E-02 at 150iterations 9.4789651E-04 2.0309448E-02 at 160iterations 5.2012643E-04 1.1774063E-02 at 170iterations 2.8793712E-04 6.0729980E-03 at 180iterations finished qdiffx linear iterations at : 17:09:12 total time elapsed so far: 17.89000 # loops : 180 mean,max change (kT/e) : 2.8793712E-04 6.0729980E-03 energy calculations done at 17.89000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.11000 DelPhi exited at 17:09:12 18.114u 0.523s 0:18.95 98.3% 0+0k 0+0io 0pf+0w