Mon Oct 10 10:24:13 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 10:24:13 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 = 2840 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5509897 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): 16.55300 81.16400 ymin,ymax (A): 30.93700 88.78100 zmin,zma (A): -1.718000 50.06000 x,y,z range (A): 64.61100 57.84399 51.77800 scale (grids/A): 0.5509897 object centre (A): 48.85850 59.85900 24.17100 number of atom coordinates read : 2840 total number of charged atoms : 2690 net assigned charge : 7.000023 assigned positive charge : 414.9349 centred at (gu) : 88.21457 88.85361 87.08830 assigned negative charge : -407.9354 centred at (gu) : 88.11211 88.79923 86.96120 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 5790 nv = 96 ne = 84 npr = 55095 no. pairs analyzed = 55095 no. exposed pairs = 4161 no. arc points = 29778 no. surface atoms = 1377 nbur = 1463 mkacc time = 0.1300000 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 = 1.540000 m= 257 mr = 2617 m= 1 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 3420 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2888 ## 334 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 7371 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.9085133E-10 7.3003298E-10 midg,1,midg; midg,igrid,midg 2.2697481E-10 7.2848255E-10 1,midg,midg; igrid,midg,midg -2.9369079E-10 8.4396357E-10 gauss-seidel spectral radius is 0.9830176 estimated iterations to convergence 63 setup time was (sec) 0.5800000 now iterating at: 10:24:13 rms-change max change #iterations 7.2739847E-02 13.10654 at 10iterations 4.8882901E-03 0.8718300 at 20iterations 3.5858992E-04 6.1735153E-02 at 30iterations 2.9940251E-05 4.4250488E-03 at 40iterations 4.2097022E-06 4.4679642E-04 at 50iterations finished qdiffx linear iterations at : 10:24:16 total time elapsed so far: 3.230000 # loops : 50 mean,max change (kT/e) : 4.2097022E-06 4.4679642E-04 energy calculations done at 3.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.420000 DelPhi exited at 10:24:17 3.419u 0.148s 0:03.98 89.1% 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 Mon Oct 10 2011 at 10:24:17 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 = 2840 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.652969 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): 16.55300 81.16400 ymin,ymax (A): 30.93700 88.78100 zmin,zma (A): -1.718000 50.06000 x,y,z range (A): 64.61100 57.84399 51.77800 scale (grids/A): 1.652969 object centre (A): 48.85850 59.85900 24.17100 number of atom coordinates read : 2840 total number of charged atoms : 2690 net assigned charge : 7.000023 assigned positive charge : 414.9349 centred at (gu) : 84.64278 86.56046 81.26466 assigned negative charge : -407.9354 centred at (gu) : 84.33608 86.39740 80.88313 start vw surface at 0.1500000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 63075 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29778 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 18682 mr = 39442 m= 1973 mr = 11755 m= 59 mr = 808 m= 0 mr = 8 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5000000 number of dielectric boundary points 31776 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 279 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 20691 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) : 0.5509897 object centre at (A) : 48.85850 59.85900 24.17100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.0887793E-04 6.0910308E-03 midg,1,midg; midg,igrid,midg 4.8459936E-03 1.5175375E-02 1,midg,midg; igrid,midg,midg -1.4702307E-02 -7.6887254E-03 gauss-seidel spectral radius is 0.9982253 estimated iterations to convergence 189 setup time was (sec) 0.8200000 now iterating at: 10:24:18 rms-change max change #iterations 3.262722 175.9327 at 10iterations 1.362626 53.00793 at 20iterations 0.5709190 19.66476 at 30iterations 0.2395710 9.482289 at 40iterations 0.1007136 3.885284 at 50iterations 4.2068575E-02 1.560490 at 60iterations 1.7759573E-02 0.6243134 at 70iterations 7.4228663E-03 0.2803302 at 80iterations 3.1209576E-03 0.1204910 at 90iterations 1.3130865E-03 4.5368195E-02 at 100iterations 5.5360666E-04 2.1170855E-02 at 110iterations 2.3313001E-04 9.3231201E-03 at 120iterations finished qdiffx linear iterations at : 10:24:25 total time elapsed so far: 7.710000 # loops : 120 mean,max change (kT/e) : 2.3313001E-04 9.3231201E-03 energy calculations done at 7.710000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.920000 DelPhi exited at 10:24:25 7.927u 0.203s 0:08.54 95.0% 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 Mon Oct 10 2011 at 10:24:25 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 = 2840 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.479454 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): 16.55300 81.16400 ymin,ymax (A): 30.93700 88.78100 zmin,zma (A): -1.718000 50.06000 x,y,z range (A): 64.61100 57.84399 51.77800 scale (grids/A): 2.479454 object centre (A): 48.85850 59.85900 24.17100 number of atom coordinates read : 2840 total number of charged atoms : 2690 net assigned charge : 7.000023 assigned positive charge : 414.9349 centred at (gu) : 81.96392 84.84045 76.89688 assigned negative charge : -407.9354 centred at (gu) : 81.50400 84.59612 76.32465 start vw surface at 0.1600000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 146224 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29778 grid for indexing accessible points = 1.400000 m= 63786 mr = 97513 m= 18265 mr = 47708 m= 2751 mr = 12658 m= 190 mr = 1558 m= 6 mr = 68 m= 0 mr = 1 time to grow re-entrant surface = 0.6600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.190000 number of dielectric boundary points 71716 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 25 iepsmp to db, and charging done at 1.330000 number of grid points assigned charge 21507 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) : 1.652969 object centre at (A) : 48.85850 59.85900 24.17100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.0905957E-02 6.4756595E-02 midg,1,midg; midg,igrid,midg -5.2870363E-02 0.3202485 1,midg,midg; igrid,midg,midg -0.5303001 -0.3326531 gauss-seidel spectral radius is 0.9991527 estimated iterations to convergence 271 setup time was (sec) 1.520000 now iterating at: 10:24:27 rms-change max change #iterations 8.656068 292.3663 at 10iterations 4.995993 141.3343 at 20iterations 2.859317 78.06436 at 30iterations 1.616249 44.08651 at 40iterations 0.9073668 27.91749 at 50iterations 0.5086876 13.99453 at 60iterations 0.2840594 7.180004 at 70iterations 0.1581864 3.447590 at 80iterations 8.7705269E-02 2.047961 at 90iterations 4.8646599E-02 1.202549 at 100iterations 2.7018564E-02 0.6285682 at 110iterations 1.4936298E-02 0.3534708 at 120iterations 8.2720090E-03 0.1817644 at 130iterations 4.5861686E-03 0.1039721 at 140iterations 2.5273706E-03 5.5409670E-02 at 150iterations 1.3992654E-03 3.1540871E-02 at 160iterations 7.7326823E-04 1.8373489E-02 at 170iterations 4.2794293E-04 9.8667145E-03 at 180iterations finished qdiffx linear iterations at : 10:24:37 total time elapsed so far: 11.73000 # loops : 180 mean,max change (kT/e) : 4.2794293E-04 9.8667145E-03 energy calculations done at 11.73000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.91000 DelPhi exited at 10:24:38 11.915u 0.241s 0:12.53 96.9% 0+0k 0+0io 0pf+0w