Mon Oct 10 19:20:27 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 19:20:27 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2948 !!! WARNING: GLU 548 has a net charge of -2.0000 !!! WARNING: GLU 564 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6124099 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): -22.21200 35.91900 ymin,ymax (A): -3.532000 49.44600 zmin,zma (A): -5.483000 48.30200 x,y,z range (A): 58.13100 52.97800 53.78500 scale (grids/A): 0.6124099 object centre (A): 6.853499 22.95700 21.40950 number of atom coordinates read : 2948 total number of charged atoms : 2806 net assigned charge : 1.3917685E-05 assigned positive charge : 438.7302 centred at (gu) : 88.74572 90.74303 92.68409 assigned negative charge : -438.7316 centred at (gu) : 88.74496 90.69653 92.67062 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7588 nv = 96 ne = 84 npr = 56977 no. pairs analyzed = 56977 no. exposed pairs = 4166 no. arc points = 30459 no. surface atoms = 1400 nbur = 1548 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 396 mr = 3534 m= 5 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 4425 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3013 ## 283 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 9167 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.6641835E-10 1.3999746E-09 midg,1,midg; midg,igrid,midg -2.3899949E-09 3.2033141E-09 1,midg,midg; igrid,midg,midg -1.2290237E-10 -1.0507641E-12 gauss-seidel spectral radius is 0.9862467 estimated iterations to convergence 70 setup time was (sec) 0.5300000 now iterating at: 19:20:28 rms-change max change #iterations 0.1236746 17.71634 at 10iterations 1.0979120E-02 1.536842 at 20iterations 9.7983342E-04 0.1260071 at 30iterations 8.9677691E-05 1.3557434E-02 at 40iterations 8.6806585E-06 1.1997223E-03 at 50iterations finished qdiffx linear iterations at : 19:20:30 total time elapsed so far: 2.950000 # loops : 50 mean,max change (kT/e) : 8.6806585E-06 1.1997223E-03 energy calculations done at 2.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.130000 DelPhi exited at 19:20:31 3.132u 0.136s 0:03.87 84.2% 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 19:20:31 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2948 !!! WARNING: GLU 548 has a net charge of -2.0000 !!! WARNING: GLU 564 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.837230 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): -22.21200 35.91900 ymin,ymax (A): -3.532000 49.44600 zmin,zma (A): -5.483000 48.30200 x,y,z range (A): 58.13100 52.97800 53.78500 scale (grids/A): 1.837230 object centre (A): 6.853499 22.95700 21.40950 number of atom coordinates read : 2948 total number of charged atoms : 2806 net assigned charge : 1.3917685E-05 assigned positive charge : 438.7302 centred at (gu) : 86.23645 92.22828 98.05146 assigned negative charge : -438.7316 centred at (gu) : 86.23457 92.08927 98.01151 start vw surface at 0.1500000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 80589 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30459 grid for indexing accessible points = 1.400000 m= 26510 mr = 50805 m= 4035 mr = 17756 m= 228 mr = 2178 m= 4 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 257 time to turn everything in is 0.5300000 number of dielectric boundary points 40587 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 219 iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 21950 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) : 0.6124099 object centre at (A) : 6.853499 22.95700 21.40950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.6835982E-04 -2.3628326E-02 midg,1,midg; midg,igrid,midg 1.7296557E-03 2.6343497E-02 1,midg,midg; igrid,midg,midg -2.5195586E-02 -3.7481498E-02 gauss-seidel spectral radius is 0.9986069 estimated iterations to convergence 212 setup time was (sec) 0.8000000 now iterating at: 19:20:32 rms-change max change #iterations 4.274025 172.6558 at 10iterations 1.958420 66.09636 at 20iterations 0.9089326 29.73451 at 30iterations 0.4228041 13.12971 at 40iterations 0.1950494 6.429804 at 50iterations 9.0408757E-02 2.823293 at 60iterations 4.1894618E-02 1.310604 at 70iterations 1.9443924E-02 0.7427454 at 80iterations 9.0381466E-03 0.2871790 at 90iterations 4.1982960E-03 0.1357422 at 100iterations 1.9439948E-03 6.3671112E-02 at 110iterations 9.0637489E-04 3.0590057E-02 at 120iterations finished qdiffx linear iterations at : 19:20:38 total time elapsed so far: 6.980000 # loops : 120 mean,max change (kT/e) : 9.0637489E-04 3.0590057E-02 energy calculations done at 6.980000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.150000 DelPhi exited at 19:20:39 7.155u 0.169s 0:07.84 93.2% 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 19:20:39 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2948 !!! WARNING: GLU 548 has a net charge of -2.0000 !!! WARNING: GLU 564 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.755845 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): -22.21200 35.91900 ymin,ymax (A): -3.532000 49.44600 zmin,zma (A): -5.483000 48.30200 x,y,z range (A): 58.13100 52.97800 53.78500 scale (grids/A): 2.755845 object centre (A): 6.853499 22.95700 21.40950 number of atom coordinates read : 2948 total number of charged atoms : 2806 net assigned charge : 1.3917685E-05 assigned positive charge : 438.7302 centred at (gu) : 84.35445 93.34211 102.0769 assigned negative charge : -438.7316 centred at (gu) : 84.35192 93.13396 102.0171 start vw surface at 0.1600000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 186396 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30459 grid for indexing accessible points = 1.400000 m= 85811 mr = 124896 m= 29961 mr = 65953 m= 7003 mr = 22321 m= 980 mr = 4878 m= 66 mr = 593 m= 1 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.7900000 no. cavity mid-points inaccessible to solvent = 772 time to turn everything in is 1.360000 number of dielectric boundary points 91565 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.490000 number of grid points assigned charge 22444 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) : 1.837230 object centre at (A) : 6.853499 22.95700 21.40950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.6946293E-03 -0.4726898 midg,1,midg; midg,igrid,midg -3.6213458E-02 0.2573281 1,midg,midg; igrid,midg,midg -0.1968586 -0.8071247 gauss-seidel spectral radius is 0.9992947 estimated iterations to convergence 297 setup time was (sec) 1.640000 now iterating at: 19:20:41 rms-change max change #iterations 10.40129 352.1014 at 10iterations 6.295034 136.0275 at 20iterations 3.761760 81.42570 at 30iterations 2.244068 46.17038 at 40iterations 1.328609 26.68500 at 50iterations 0.7846335 18.22995 at 60iterations 0.4623516 9.659575 at 70iterations 0.2711107 6.035051 at 80iterations 0.1592103 3.208243 at 90iterations 9.3254708E-02 1.844558 at 100iterations 5.4461446E-02 1.030315 at 110iterations 3.1912677E-02 0.6201897 at 120iterations 1.8603329E-02 0.3407879 at 130iterations 1.0870266E-02 0.2112503 at 140iterations 6.3420823E-03 0.1185417 at 150iterations 3.6994701E-03 6.7887664E-02 at 160iterations 2.1623326E-03 4.2305946E-02 at 170iterations 1.2596910E-03 2.1913528E-02 at 180iterations finished qdiffx linear iterations at : 19:20:51 total time elapsed so far: 11.20000 # loops : 180 mean,max change (kT/e) : 1.2596910E-03 2.1913528E-02 energy calculations done at 11.20000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.38000 DelPhi exited at 19:20:51 11.379u 0.165s 0:12.03 95.8% 0+0k 0+0io 0pf+0w