Mon Oct 10 14:01:21 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 14:01:21 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2117 !!! WARNING: LYS 224 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.7450037 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): -21.26800 24.06800 ymin,ymax (A): -8.044000 36.24400 zmin,zma (A): -3.420000 44.36500 x,y,z range (A): 45.33600 44.28800 47.78500 scale (grids/A): 0.7450037 object centre (A): 1.400000 14.10000 20.47250 number of atom coordinates read : 2117 total number of charged atoms : 1978 net assigned charge : -6.271980 assigned positive charge : 317.0999 centred at (gu) : 89.18422 90.45085 90.09136 assigned negative charge : -323.3720 centred at (gu) : 89.21121 90.54932 90.28255 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 8030 nv = 96 ne = 84 npr = 43929 no. pairs analyzed = 43929 no. exposed pairs = 2660 no. arc points = 19147 no. surface atoms = 893 nbur = 1224 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 603 mr = 4432 m= 2 mr = 131 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 68 time to turn everything in is 0.2900000 number of dielectric boundary points 4072 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1552 ## 144 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 8508 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.9201471E-08 -3.4924648E-07 midg,1,midg; midg,igrid,midg -1.1156644E-08 -2.5558438E-07 1,midg,midg; igrid,midg,midg -1.0581818E-07 -1.3204266E-07 gauss-seidel spectral radius is 0.9906121 estimated iterations to convergence 84 setup time was (sec) 0.7000000 now iterating at: 14:01:23 rms-change max change #iterations 0.2501860 39.47494 at 10iterations 3.4755569E-02 4.384561 at 20iterations 4.6712039E-03 0.5979128 at 30iterations 6.3392235E-04 8.7371826E-02 at 40iterations 8.6265296E-05 1.0284424E-02 at 50iterations finished qdiffx linear iterations at : 14:01:29 total time elapsed so far: 7.570000 # loops : 50 mean,max change (kT/e) : 8.6265296E-05 1.0284424E-02 energy calculations done at 7.570000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.750000 DelPhi exited at 14:01:30 7.757u 0.656s 0:09.04 92.9% 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 14:01:30 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2117 !!! WARNING: LYS 224 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.235011 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): -21.26800 24.06800 ymin,ymax (A): -8.044000 36.24400 zmin,zma (A): -3.420000 44.36500 x,y,z range (A): 45.33600 44.28800 47.78500 scale (grids/A): 2.235011 object centre (A): 1.400000 14.10000 20.47250 number of atom coordinates read : 2117 total number of charged atoms : 1978 net assigned charge : -6.271980 assigned positive charge : 317.0999 centred at (gu) : 87.55242 91.35238 90.27437 assigned negative charge : -323.3720 centred at (gu) : 87.63353 91.64786 90.84743 start vw surface at 0.1200000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 84352 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19147 grid for indexing accessible points = 1.400000 m= 33989 mr = 57921 m= 7522 mr = 25929 m= 873 mr = 5315 m= 23 mr = 524 m= 0 mr = 4 time to grow re-entrant surface = 0.4100000 no. cavity mid-points inaccessible to solvent = 1861 time to turn everything in is 0.8000000 number of dielectric boundary points 37066 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 47 iepsmp to db, and charging done at 1.000000 number of grid points assigned charge 15752 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) : 0.7450037 object centre at (A) : 1.400000 14.10000 20.47250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.1035230E-03 -0.1374011 midg,1,midg; midg,igrid,midg -2.6576040E-02 -4.0335961E-02 1,midg,midg; igrid,midg,midg -2.1129039E-03 -1.0881599E-02 gauss-seidel spectral radius is 0.9989384 estimated iterations to convergence 243 setup time was (sec) 1.310000 now iterating at: 14:01:32 rms-change max change #iterations 5.137473 236.8955 at 10iterations 2.611964 81.40009 at 20iterations 1.335398 40.92725 at 30iterations 0.6856132 21.87728 at 40iterations 0.3487118 10.42431 at 50iterations 0.1788630 5.246341 at 60iterations 9.1522150E-02 2.831774 at 70iterations 4.6623748E-02 1.297607 at 80iterations 2.3994949E-02 0.6095047 at 90iterations 1.2300685E-02 0.3580704 at 100iterations 6.2742890E-03 0.1841047 at 110iterations 3.2187807E-03 8.7429523E-02 at 120iterations finished qdiffx linear iterations at : 14:01:49 total time elapsed so far: 18.00000 # loops : 120 mean,max change (kT/e) : 3.2187807E-03 8.7429523E-02 energy calculations done at 18.00000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.18000 DelPhi exited at 14:01:49 18.184u 0.763s 0:19.24 98.4% 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 14:01:50 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2117 !!! WARNING: LYS 224 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 3.352517 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): -21.26800 24.06800 ymin,ymax (A): -8.044000 36.24400 zmin,zma (A): -3.420000 44.36500 x,y,z range (A): 45.33600 44.28800 47.78500 scale (grids/A): 3.352517 object centre (A): 1.400000 14.10000 20.47250 number of atom coordinates read : 2117 total number of charged atoms : 1978 net assigned charge : -6.271980 assigned positive charge : 317.0999 centred at (gu) : 86.32861 92.02872 90.41144 assigned negative charge : -323.3720 centred at (gu) : 86.45027 92.47177 91.27129 start vw surface at 0.1100000 fill in re-entrant regions at 0.9500000 boundary points on vw surface= 193924 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19147 grid for indexing accessible points = 1.400000 m= 103749 mr = 139376 m= 45098 mr = 86045 m= 14577 mr = 37631 m= 3509 mr = 11665 m= 503 mr = 2807 m= 29 mr = 378 m= 0 mr = 14 time to grow re-entrant surface = 1.330000 no. cavity mid-points inaccessible to solvent = 6272 time to turn everything in is 2.470000 number of dielectric boundary points 83473 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.720000 number of grid points assigned charge 15824 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) : 2.235011 object centre at (A) : 1.400000 14.10000 20.47250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.4733305E-03 -1.243806 midg,1,midg; midg,igrid,midg -0.2445163 -0.2033155 1,midg,midg; igrid,midg,midg 8.4002458E-02 -0.2065133 gauss-seidel spectral radius is 0.9993207 estimated iterations to convergence 303 setup time was (sec) 3.040000 now iterating at: 14:01:53 rms-change max change #iterations 11.05505 368.7083 at 10iterations 6.514048 116.0329 at 20iterations 3.834776 66.50863 at 30iterations 2.249946 37.04580 at 40iterations 1.324476 23.03040 at 50iterations 0.7771707 11.94090 at 60iterations 0.4568894 7.268453 at 70iterations 0.2684313 4.532977 at 80iterations 0.1578540 2.530701 at 90iterations 9.3011208E-02 1.571766 at 100iterations 5.4399461E-02 0.8612142 at 110iterations 3.1923123E-02 0.6000690 at 120iterations 1.8779427E-02 0.2961168 at 130iterations 1.1035745E-02 0.1781578 at 140iterations 6.4655328E-03 0.1053724 at 150iterations 3.8017570E-03 6.0864925E-02 at 160iterations 2.2342133E-03 3.5461426E-02 at 170iterations 1.3165664E-03 2.1748304E-02 at 180iterations finished qdiffx linear iterations at : 14:02:20 total time elapsed so far: 30.14000 # loops : 180 mean,max change (kT/e) : 1.3165664E-03 2.1748304E-02 energy calculations done at 30.14000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 30.31000 DelPhi exited at 14:02:22 30.310u 0.807s 0:32.09 96.9% 0+0k 0+0io 0pf+0w