Tue Oct 11 03:49:06 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 Tue Oct 11 2011 at 03:49:06 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2730 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 0.6607153 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): -11.00300 36.65300 ymin,ymax (A): -25.78900 22.67100 zmin,zma (A): -8.522000 45.35900 x,y,z range (A): 47.65600 48.46000 53.88100 scale (grids/A): 0.6607153 object centre (A): 12.82500 -1.559000 18.41850 number of atom coordinates read : 2730 total number of charged atoms : 2578 net assigned charge : 1.140015 assigned positive charge : 410.9278 centred at (gu) : 90.05379 90.24528 91.37664 assigned negative charge : -409.7884 centred at (gu) : 89.80294 90.11847 91.32945 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 7958 nv = 96 ne = 84 npr = 56305 no. pairs analyzed = 56305 no. exposed pairs = 3304 no. arc points = 23264 no. surface atoms = 1110 nbur = 1620 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 448 mr = 4551 m= 5 mr = 55 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 32 time to turn everything in is 0.3300000 number of dielectric boundary points 3805 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2212 ## 201 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 9422 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.4218701E-09 1.7066016E-08 midg,1,midg; midg,igrid,midg -2.3273484E-08 3.0927268E-08 1,midg,midg; igrid,midg,midg -5.1367092E-08 5.5313517E-08 gauss-seidel spectral radius is 0.9881349 estimated iterations to convergence 75 setup time was (sec) 0.6100000 now iterating at: 03:49:07 rms-change max change #iterations 0.1721630 23.71654 at 10iterations 1.8544367E-02 2.546916 at 20iterations 2.0962362E-03 0.2595825 at 30iterations 2.8220049E-04 4.9205780E-02 at 40iterations 5.6468511E-05 7.4348450E-03 at 50iterations finished qdiffx linear iterations at : 03:49:11 total time elapsed so far: 4.430000 # loops : 50 mean,max change (kT/e) : 5.6468511E-05 7.4348450E-03 energy calculations done at 4.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.590000 DelPhi exited at 03:49:12 4.597u 0.426s 0:05.82 86.0% 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 Tue Oct 11 2011 at 03:49:12 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2730 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 1.982146 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): -11.00300 36.65300 ymin,ymax (A): -25.78900 22.67100 zmin,zma (A): -8.522000 45.35900 x,y,z range (A): 47.65600 48.46000 53.88100 scale (grids/A): 1.982146 object centre (A): 12.82500 -1.559000 18.41850 number of atom coordinates read : 2730 total number of charged atoms : 2578 net assigned charge : 1.140015 assigned positive charge : 410.9278 centred at (gu) : 90.16071 90.73524 94.12903 assigned negative charge : -409.7884 centred at (gu) : 89.40865 90.35513 93.98824 start vw surface at 0.1200000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 85354 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23264 grid for indexing accessible points = 1.400000 m= 31958 mr = 60391 m= 5225 mr = 23975 m= 318 mr = 3384 m= 6 mr = 125 m= 0 mr = 0 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 1241 time to turn everything in is 0.7000000 number of dielectric boundary points 34986 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 164 iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 20398 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) : 0.6607153 object centre at (A) : 12.82500 -1.559000 18.41850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.9508246E-02 -2.6296180E-02 midg,1,midg; midg,igrid,midg -1.4986103E-02 2.8835097E-02 1,midg,midg; igrid,midg,midg -1.6192226E-02 7.0338495E-02 gauss-seidel spectral radius is 0.9987464 estimated iterations to convergence 224 setup time was (sec) 0.9900000 now iterating at: 03:49:14 rms-change max change #iterations 4.753864 182.8824 at 10iterations 2.301005 70.69681 at 20iterations 1.111265 33.31744 at 30iterations 0.5390080 14.85627 at 40iterations 0.2615286 7.493295 at 50iterations 0.1268045 3.923186 at 60iterations 6.1449397E-02 1.856666 at 70iterations 2.9775174E-02 0.9510612 at 80iterations 1.4398506E-02 0.4502907 at 90iterations 7.0215045E-03 0.2084694 at 100iterations 3.4239173E-03 0.1064720 at 110iterations 1.6822112E-03 5.0850868E-02 at 120iterations finished qdiffx linear iterations at : 03:49:24 total time elapsed so far: 10.98000 # loops : 120 mean,max change (kT/e) : 1.6822112E-03 5.0850868E-02 energy calculations done at 10.98000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.15000 DelPhi exited at 03:49:24 11.159u 0.466s 0:11.99 96.8% 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 Tue Oct 11 2011 at 03:49:24 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2730 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 2.973219 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): -11.00300 36.65300 ymin,ymax (A): -25.78900 22.67100 zmin,zma (A): -8.522000 45.35900 x,y,z range (A): 47.65600 48.46000 53.88100 scale (grids/A): 2.973219 object centre (A): 12.82500 -1.559000 18.41850 number of atom coordinates read : 2730 total number of charged atoms : 2578 net assigned charge : 1.140015 assigned positive charge : 410.9278 centred at (gu) : 90.24113 91.10262 96.19346 assigned negative charge : -409.7884 centred at (gu) : 89.11304 90.53262 95.98219 start vw surface at 0.1200000 fill in re-entrant regions at 0.5900000 boundary points on vw surface= 197193 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23264 grid for indexing accessible points = 1.400000 m= 102470 mr = 145959 m= 38381 mr = 84674 m= 9455 mr = 31233 m= 1446 mr = 7266 m= 108 mr = 995 m= 3 mr = 44 m= 0 mr = 0 time to grow re-entrant surface = 1.150000 no. cavity mid-points inaccessible to solvent = 4274 time to turn everything in is 1.860000 number of dielectric boundary points 78885 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.990000 number of grid points assigned charge 20617 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) : 1.982146 object centre at (A) : 12.82500 -1.559000 18.41850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.7591190 -7.9956852E-02 midg,1,midg; midg,igrid,midg -0.1845022 0.3573939 1,midg,midg; igrid,midg,midg -9.0991616E-02 0.5938196 gauss-seidel spectral radius is 0.9992843 estimated iterations to convergence 295 setup time was (sec) 2.190000 now iterating at: 03:49:27 rms-change max change #iterations 10.86915 415.8813 at 10iterations 6.386959 130.2195 at 20iterations 3.742635 72.31884 at 30iterations 2.192326 42.35832 at 40iterations 1.281726 24.20027 at 50iterations 0.7491368 14.27105 at 60iterations 0.4367629 8.951708 at 70iterations 0.2547108 4.522186 at 80iterations 0.1485432 2.598248 at 90iterations 8.6461425E-02 1.402548 at 100iterations 5.0342452E-02 0.9783401 at 110iterations 2.9334689E-02 0.4965897 at 120iterations 1.7121764E-02 0.3641548 at 130iterations 1.0072172E-02 0.1607840 at 140iterations 5.9369104E-03 0.1050568 at 150iterations 3.5464235E-03 6.7689896E-02 at 160iterations 2.1633434E-03 4.2968750E-02 at 170iterations 1.3548984E-03 2.6178360E-02 at 180iterations finished qdiffx linear iterations at : 03:49:44 total time elapsed so far: 18.84000 # loops : 180 mean,max change (kT/e) : 1.3548984E-03 2.6178360E-02 energy calculations done at 18.84000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.01000 DelPhi exited at 03:49:44 19.013u 0.494s 0:19.94 97.7% 0+0k 0+0io 0pf+0w