Tue Oct 11 07:18:24 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 07:18:24 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: 243 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3301 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5987419 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): 0.3019999 48.42800 ymin,ymax (A): -8.468000 48.41400 zmin,zma (A): 1.256000 60.71400 x,y,z range (A): 48.12600 56.88200 59.45800 scale (grids/A): 0.5987419 object centre (A): 24.36500 19.97300 30.98500 number of atom coordinates read : 3301 total number of charged atoms : 3150 net assigned charge : 8.6724758E-06 assigned positive charge : 494.9666 centred at (gu) : 89.95305 89.85870 90.61395 assigned negative charge : -494.9679 centred at (gu) : 89.88313 89.81929 90.57616 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 7745 nv = 96 ne = 84 npr = 68093 no. pairs analyzed = 68093 no. exposed pairs = 3831 no. arc points = 26215 no. surface atoms = 1296 nbur = 2005 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 359 mr = 4504 m= 1 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 36 time to turn everything in is 0.3900000 number of dielectric boundary points 3570 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2709 ## 265 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 9819 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.4797087E-09 1.9365491E-09 midg,1,midg; midg,igrid,midg -1.8377585E-09 1.6945411E-09 1,midg,midg; igrid,midg,midg -3.1965830E-09 3.0661857E-09 gauss-seidel spectral radius is 0.9856160 estimated iterations to convergence 68 setup time was (sec) 0.6300000 now iterating at: 07:18:25 rms-change max change #iterations 0.1208147 19.31660 at 10iterations 1.0517480E-02 1.533436 at 20iterations 9.9096296E-04 0.1374025 at 30iterations 1.2393731E-04 2.1991730E-02 at 40iterations 2.1973645E-05 4.3239594E-03 at 50iterations finished qdiffx linear iterations at : 07:18:28 total time elapsed so far: 3.420000 # loops : 50 mean,max change (kT/e) : 2.1973645E-05 4.3239594E-03 energy calculations done at 3.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.610000 DelPhi exited at 07:18:29 3.616u 0.153s 0:04.25 88.4% 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 Tue Oct 11 2011 at 07:18:29 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: 243 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3301 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.796226 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): 0.3019999 48.42800 ymin,ymax (A): -8.468000 48.41400 zmin,zma (A): 1.256000 60.71400 x,y,z range (A): 48.12600 56.88200 59.45800 scale (grids/A): 1.796226 object centre (A): 24.36500 19.97300 30.98500 number of atom coordinates read : 3301 total number of charged atoms : 3150 net assigned charge : 8.6724758E-06 assigned positive charge : 494.9666 centred at (gu) : 89.85825 89.57539 91.84098 assigned negative charge : -494.9679 centred at (gu) : 89.64920 89.45752 91.72762 start vw surface at 0.1800000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 85188 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26215 grid for indexing accessible points = 1.400000 m= 29777 mr = 61237 m= 4001 mr = 22486 m= 188 mr = 2515 m= 2 mr = 70 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 3523 time to turn everything in is 0.6400000 number of dielectric boundary points 32848 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 216 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 24585 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) : 0.5987419 object centre at (A) : 24.36500 19.97300 30.98500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.8886053E-03 9.0049244E-03 midg,1,midg; midg,igrid,midg -1.5273885E-02 2.1288693E-03 1,midg,midg; igrid,midg,midg -5.5677462E-03 1.8930889E-03 gauss-seidel spectral radius is 0.9985346 estimated iterations to convergence 207 setup time was (sec) 0.9300000 now iterating at: 07:18:30 rms-change max change #iterations 4.330758 200.2205 at 10iterations 1.968915 60.11438 at 20iterations 0.8967731 26.61654 at 30iterations 0.4104203 13.02218 at 40iterations 0.1874621 6.208271 at 50iterations 8.5801683E-02 2.614161 at 60iterations 3.9251242E-02 1.169720 at 70iterations 1.7887533E-02 0.5183716 at 80iterations 8.1659872E-03 0.2453346 at 90iterations 3.7301062E-03 0.1234055 at 100iterations 1.7067028E-03 5.6518555E-02 at 110iterations 7.8233634E-04 2.4034500E-02 at 120iterations finished qdiffx linear iterations at : 07:18:37 total time elapsed so far: 7.860000 # loops : 120 mean,max change (kT/e) : 7.8233634E-04 2.4034500E-02 energy calculations done at 7.860000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.050000 DelPhi exited at 07:18:37 8.051u 0.198s 0:08.53 96.6% 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 Tue Oct 11 2011 at 07:18:37 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: 243 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3301 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.694339 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): 0.3019999 48.42800 ymin,ymax (A): -8.468000 48.41400 zmin,zma (A): 1.256000 60.71400 x,y,z range (A): 48.12600 56.88200 59.45800 scale (grids/A): 2.694339 object centre (A): 24.36500 19.97300 30.98500 number of atom coordinates read : 3301 total number of charged atoms : 3150 net assigned charge : 8.6724758E-06 assigned positive charge : 494.9666 centred at (gu) : 89.78715 89.36293 92.76138 assigned negative charge : -494.9679 centred at (gu) : 89.47371 89.18616 92.59140 start vw surface at 0.1800000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 197700 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26215 grid for indexing accessible points = 1.400000 m= 99456 mr = 148334 m= 33042 mr = 82677 m= 6959 mr = 26977 m= 830 mr = 5289 m= 47 mr = 576 m= 0 mr = 26 time to grow re-entrant surface = 0.9000000 no. cavity mid-points inaccessible to solvent = 12031 time to turn everything in is 1.580000 number of dielectric boundary points 74155 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.740000 number of grid points assigned charge 25196 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) : 1.796226 object centre at (A) : 24.36500 19.97300 30.98500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1489896 -3.4062639E-02 midg,1,midg; midg,igrid,midg -0.2160993 1.8599972E-02 1,midg,midg; igrid,midg,midg -5.7814099E-02 2.4729082E-03 gauss-seidel spectral radius is 0.9992388 estimated iterations to convergence 286 setup time was (sec) 1.920000 now iterating at: 07:18:39 rms-change max change #iterations 10.32318 280.4807 at 10iterations 5.960581 138.5831 at 20iterations 3.424038 99.27610 at 30iterations 1.955606 35.11535 at 40iterations 1.121545 22.47249 at 50iterations 0.6414878 11.58477 at 60iterations 0.3664243 7.139643 at 70iterations 0.2089160 3.694276 at 80iterations 0.1192543 2.130592 at 90iterations 6.8115152E-02 1.115322 at 100iterations 3.8872480E-02 0.6585407 at 110iterations 2.2132134E-02 0.4124870 at 120iterations 1.2631339E-02 0.2211113 at 130iterations 7.2128037E-03 0.1363373 at 140iterations 4.1156285E-03 6.5712452E-02 at 150iterations 2.3618864E-03 3.8991928E-02 at 160iterations 1.3612034E-03 2.4448395E-02 at 170iterations 7.8532932E-04 1.4447212E-02 at 180iterations finished qdiffx linear iterations at : 07:18:51 total time elapsed so far: 13.15000 # loops : 180 mean,max change (kT/e) : 7.8532932E-04 1.4447212E-02 energy calculations done at 13.15000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.33000 DelPhi exited at 07:18:51 13.335u 0.242s 0:14.01 96.8% 0+0k 0+0io 0pf+0w