Sun Oct 9 00:52:29 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 Sun Oct 9 2011 at 00:52:29 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2187 !!! WARNING: HIT 84 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6520266 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): -0.2310001 54.36800 ymin,ymax (A): -15.86500 27.58200 zmin,zma (A): 32.18900 83.80099 x,y,z range (A): 54.59900 43.44700 51.61200 scale (grids/A): 0.6520266 object centre (A): 27.06850 5.858500 57.99500 number of atom coordinates read : 2187 total number of charged atoms : 2053 net assigned charge : 11.51402 assigned positive charge : 319.9968 centred at (gu) : 90.33285 88.85745 88.58683 assigned negative charge : -308.4832 centred at (gu) : 90.37477 88.92531 88.65484 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6341 nv = 96 ne = 84 npr = 43695 no. pairs analyzed = 43695 no. exposed pairs = 2833 no. arc points = 20495 no. surface atoms = 951 nbur = 1236 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 354 mr = 3295 m= 2 mr = 57 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 59 time to turn everything in is 0.2700000 number of dielectric boundary points 3345 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2012 ## 188 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 7476 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.2702482E-08 1.1018563E-08 midg,1,midg; midg,igrid,midg 4.0327016E-08 1.1624736E-08 1,midg,midg; igrid,midg,midg 2.6672035E-08 1.9086364E-08 gauss-seidel spectral radius is 0.9877816 estimated iterations to convergence 74 setup time was (sec) 0.4900000 now iterating at: 00:52:30 rms-change max change #iterations 0.1458862 22.42705 at 10iterations 1.4993347E-02 2.184734 at 20iterations 1.5497694E-03 0.2302837 at 30iterations 1.5652024E-04 2.5866508E-02 at 40iterations 1.6578342E-05 2.2125244E-03 at 50iterations finished qdiffx linear iterations at : 00:52:32 total time elapsed so far: 2.970000 # loops : 50 mean,max change (kT/e) : 1.6578342E-05 2.2125244E-03 energy calculations done at 2.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.150000 DelPhi exited at 00:52:33 3.153u 0.152s 0:03.59 91.9% 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 Sun Oct 9 2011 at 00:52:33 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2187 !!! WARNING: HIT 84 has a net charge of 0.5140 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: 1.956080 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): -0.2310001 54.36800 ymin,ymax (A): -15.86500 27.58200 zmin,zma (A): 32.18900 83.80099 x,y,z range (A): 54.59900 43.44700 51.61200 scale (grids/A): 1.956080 object centre (A): 27.06850 5.858500 57.99500 number of atom coordinates read : 2187 total number of charged atoms : 2053 net assigned charge : 11.51402 assigned positive charge : 319.9968 centred at (gu) : 90.99845 86.57236 85.76040 assigned negative charge : -308.4832 centred at (gu) : 91.12445 86.77612 85.96471 start vw surface at 0.1500000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 67695 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20495 grid for indexing accessible points = 1.400000 m= 24154 mr = 45057 m= 4221 mr = 17500 m= 320 mr = 2689 m= 8 mr = 169 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 2766 time to turn everything in is 0.5000000 number of dielectric boundary points 30983 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 138 iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 16186 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) : 0.6520266 object centre at (A) : 27.06850 5.858500 57.99500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.4445196E-02 3.4368515E-02 midg,1,midg; midg,igrid,midg 2.9737292E-02 6.2112138E-04 1,midg,midg; igrid,midg,midg 7.0527405E-02 5.1610172E-02 gauss-seidel spectral radius is 0.9986694 estimated iterations to convergence 217 setup time was (sec) 0.7700000 now iterating at: 00:52:33 rms-change max change #iterations 3.928483 195.8437 at 10iterations 1.856259 68.56854 at 20iterations 0.8713472 30.53494 at 30iterations 0.4117280 13.33372 at 40iterations 0.1944370 6.493387 at 50iterations 9.1715127E-02 2.816116 at 60iterations 4.3328620E-02 1.400547 at 70iterations 2.0466857E-02 0.6581535 at 80iterations 9.6600885E-03 0.3443069 at 90iterations 4.5466013E-03 0.1536307 at 100iterations 2.1557522E-03 6.9730759E-02 at 110iterations 1.0174681E-03 3.2615662E-02 at 120iterations finished qdiffx linear iterations at : 00:52:41 total time elapsed so far: 8.090000 # loops : 120 mean,max change (kT/e) : 1.0174681E-03 3.2615662E-02 energy calculations done at 8.090000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.270000 DelPhi exited at 00:52:41 8.274u 0.191s 0:08.76 96.5% 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 Sun Oct 9 2011 at 00:52:41 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2187 !!! WARNING: HIT 84 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.934120 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): -0.2310001 54.36800 ymin,ymax (A): -15.86500 27.58200 zmin,zma (A): 32.18900 83.80099 x,y,z range (A): 54.59900 43.44700 51.61200 scale (grids/A): 2.934120 object centre (A): 27.06850 5.858500 57.99500 number of atom coordinates read : 2187 total number of charged atoms : 2053 net assigned charge : 11.51402 assigned positive charge : 319.9968 centred at (gu) : 91.49770 84.85848 83.64050 assigned negative charge : -308.4832 centred at (gu) : 91.68670 85.16418 83.94696 start vw surface at 0.1500000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 156281 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20495 grid for indexing accessible points = 1.400000 m= 76916 mr = 109462 m= 28796 mr = 61785 m= 7817 mr = 23134 m= 1501 mr = 5938 m= 153 mr = 1129 m= 3 mr = 95 m= 0 mr = 2 time to grow re-entrant surface = 0.6900001 no. cavity mid-points inaccessible to solvent = 9184 time to turn everything in is 1.220000 number of dielectric boundary points 69922 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.360000 number of grid points assigned charge 16424 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) : 1.956080 object centre at (A) : 27.06850 5.858500 57.99500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3357497 0.4850229 midg,1,midg; midg,igrid,midg 0.2594809 5.5729743E-04 1,midg,midg; igrid,midg,midg 0.8890426 0.4904425 gauss-seidel spectral radius is 0.9992696 estimated iterations to convergence 292 setup time was (sec) 1.520000 now iterating at: 00:52:43 rms-change max change #iterations 9.284072 395.6615 at 10iterations 5.485345 176.5605 at 20iterations 3.202571 78.21067 at 30iterations 1.864725 49.23544 at 40iterations 1.086559 24.61458 at 50iterations 0.6283665 13.68913 at 60iterations 0.3647499 6.697258 at 70iterations 0.2102932 3.746521 at 80iterations 0.1216510 2.427341 at 90iterations 7.0369318E-02 1.262392 at 100iterations 4.0531348E-02 0.8891401 at 110iterations 2.3408135E-02 0.4949188 at 120iterations 1.3505638E-02 0.2522278 at 130iterations 7.7742371E-03 0.1510229 at 140iterations 4.4814851E-03 8.1186295E-02 at 150iterations 2.5770084E-03 4.9251378E-02 at 160iterations 1.4876103E-03 2.8016090E-02 at 170iterations 8.5659022E-04 1.7183304E-02 at 180iterations finished qdiffx linear iterations at : 00:52:53 total time elapsed so far: 11.88000 # loops : 180 mean,max change (kT/e) : 8.5659022E-04 1.7183304E-02 energy calculations done at 11.88000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.06000 DelPhi exited at 00:52:54 12.058u 0.191s 0:12.52 97.7% 0+0k 0+0io 0pf+0w