Sun Oct 9 08:11:45 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 08:11:46 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: 322 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3454 !!! WARNING: NAP 1080 has a net charge of -2.0000 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: 0.5411156 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): 12.30900 78.09900 ymin,ymax (A): 27.32500 79.70800 zmin,zma (A): 61.74800 117.5210 x,y,z range (A): 65.79000 52.38300 55.77301 scale (grids/A): 0.5411156 object centre (A): 45.20400 53.51650 89.63450 number of atom coordinates read : 3454 total number of charged atoms : 3311 net assigned charge : 9.000023 assigned positive charge : 525.4616 centred at (gu) : 89.58394 90.39360 87.40749 assigned negative charge : -516.4631 centred at (gu) : 89.67322 90.44312 87.42664 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 6582 nv = 96 ne = 84 npr = 68993 no. pairs analyzed = 68993 no. exposed pairs = 4244 no. arc points = 30357 no. surface atoms = 1418 nbur = 2036 mkacc time = 0.1900000 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 = 1.568000 m= 255 mr = 3485 m= 1 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 24 time to turn everything in is 0.4100000 number of dielectric boundary points 3344 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3079 ## 415 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 8713 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0959598E-09 1.8068598E-10 midg,1,midg; midg,igrid,midg 6.9645584E-10 1.4856601E-10 1,midg,midg; igrid,midg,midg 1.1271302E-09 -1.0706400E-10 gauss-seidel spectral radius is 0.9824314 estimated iterations to convergence 62 setup time was (sec) 0.6900000 now iterating at: 08:11:46 rms-change max change #iterations 7.5711787E-02 14.06941 at 10iterations 5.0462978E-03 0.7395401 at 20iterations 3.7770052E-04 4.9737453E-02 at 30iterations 4.7725953E-05 6.7043304E-03 at 40iterations 9.3406006E-06 1.2854338E-03 at 50iterations finished qdiffx linear iterations at : 08:11:50 total time elapsed so far: 3.980000 # loops : 50 mean,max change (kT/e) : 9.3406006E-06 1.2854338E-03 energy calculations done at 3.980000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.160000 DelPhi exited at 08:11:50 4.161u 0.256s 0:04.69 94.0% 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 Sun Oct 9 2011 at 08:11:50 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: 322 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3454 !!! WARNING: NAP 1080 has a net charge of -2.0000 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: 1.623347 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): 12.30900 78.09900 ymin,ymax (A): 27.32500 79.70800 zmin,zma (A): 61.74800 117.5210 x,y,z range (A): 65.79000 52.38300 55.77301 scale (grids/A): 1.623347 object centre (A): 45.20400 53.51650 89.63450 number of atom coordinates read : 3454 total number of charged atoms : 3311 net assigned charge : 9.000023 assigned positive charge : 525.4616 centred at (gu) : 88.75098 91.18000 82.22153 assigned negative charge : -516.4631 centred at (gu) : 89.01918 91.32882 82.27962 start vw surface at 0.1900000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 73243 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30357 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 21821 mr = 50240 m= 2081 mr = 14933 m= 51 mr = 1030 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 1249 time to turn everything in is 0.6500000 number of dielectric boundary points 30993 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 332 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 25304 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) : 0.5411156 object centre at (A) : 45.20400 53.51650 89.63450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3754902E-02 8.4768003E-03 midg,1,midg; midg,igrid,midg 1.2338839E-02 -3.8384802E-03 1,midg,midg; igrid,midg,midg 2.5405452E-02 2.5338843E-03 gauss-seidel spectral radius is 0.9982101 estimated iterations to convergence 188 setup time was (sec) 0.9500000 now iterating at: 08:11:51 rms-change max change #iterations 3.566364 147.0060 at 10iterations 1.493800 53.97966 at 20iterations 0.6288772 25.35520 at 30iterations 0.2636540 9.491035 at 40iterations 0.1108439 4.365582 at 50iterations 4.6707395E-02 1.709614 at 60iterations 1.9644693E-02 0.6943846 at 70iterations 8.2278363E-03 0.2949615 at 80iterations 3.4756863E-03 0.1126671 at 90iterations 1.4635667E-03 4.8629761E-02 at 100iterations 6.1963848E-04 2.1470070E-02 at 110iterations 2.6438507E-04 9.3231201E-03 at 120iterations finished qdiffx linear iterations at : 08:12:00 total time elapsed so far: 9.160000 # loops : 120 mean,max change (kT/e) : 2.6438507E-04 9.3231201E-03 energy calculations done at 9.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.330000 DelPhi exited at 08:12:00 9.335u 0.287s 0:09.90 97.0% 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 Sun Oct 9 2011 at 08:12:00 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: 322 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3454 !!! WARNING: NAP 1080 has a net charge of -2.0000 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: 2.435020 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): 12.30900 78.09900 ymin,ymax (A): 27.32500 79.70800 zmin,zma (A): 61.74800 117.5210 x,y,z range (A): 65.79000 52.38300 55.77301 scale (grids/A): 2.435020 object centre (A): 45.20400 53.51650 89.63450 number of atom coordinates read : 3454 total number of charged atoms : 3311 net assigned charge : 9.000023 assigned positive charge : 525.4616 centred at (gu) : 88.12634 91.76976 78.33199 assigned negative charge : -516.4631 centred at (gu) : 88.52873 91.99313 78.41943 start vw surface at 0.1800000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 170648 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30357 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 76814 mr = 123469 m= 20811 mr = 60617 m= 3274 mr = 15503 m= 231 mr = 2182 m= 1 mr = 75 m= 0 mr = 0 time to grow re-entrant surface = 0.9200000 no. cavity mid-points inaccessible to solvent = 4023 time to turn everything in is 1.560000 number of dielectric boundary points 69933 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 32 iepsmp to db, and charging done at 1.720000 number of grid points assigned charge 26445 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) : 1.623347 object centre at (A) : 45.20400 53.51650 89.63450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2000457 0.1248968 midg,1,midg; midg,igrid,midg 0.1820251 -5.8981977E-02 1,midg,midg; igrid,midg,midg 0.4208403 2.6139226E-02 gauss-seidel spectral radius is 0.9991544 estimated iterations to convergence 272 setup time was (sec) 1.890000 now iterating at: 08:12:02 rms-change max change #iterations 9.338378 349.7601 at 10iterations 5.301111 156.7206 at 20iterations 2.990175 77.64510 at 30iterations 1.681500 41.27767 at 40iterations 0.9394621 21.64032 at 50iterations 0.5238627 12.42952 at 60iterations 0.2912541 6.054855 at 70iterations 0.1616242 3.732689 at 80iterations 8.9885563E-02 2.154317 at 90iterations 4.9987238E-02 1.020580 at 100iterations 2.7601415E-02 0.5468807 at 110iterations 1.5313407E-02 0.2957168 at 120iterations 8.4884809E-03 0.1639709 at 130iterations 4.7041671E-03 0.1037986 at 140iterations 2.6029374E-03 5.4007530E-02 at 150iterations 1.4391509E-03 3.0471683E-02 at 160iterations 7.9628697E-04 1.6029358E-02 at 170iterations 4.4200526E-04 8.5639954E-03 at 180iterations finished qdiffx linear iterations at : 08:12:16 total time elapsed so far: 15.28000 # loops : 180 mean,max change (kT/e) : 4.4200526E-04 8.5639954E-03 energy calculations done at 15.28000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.45000 DelPhi exited at 08:12:16 15.456u 0.303s 0:16.02 98.3% 0+0k 0+0io 0pf+0w