Tue Oct 11 03:20:05 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 03:20:05 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 = 2473 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6082039 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): -37.45700 11.88900 ymin,ymax (A): -53.03400 1.908000 zmin,zma (A): -55.77600 2.757000 x,y,z range (A): 49.34600 54.94200 58.53300 scale (grids/A): 0.6082039 object centre (A): -12.78400 -25.56300 -26.50950 number of atom coordinates read : 2473 total number of charged atoms : 2326 net assigned charge : -0.4999910 assigned positive charge : 363.9521 centred at (gu) : 91.37599 87.28316 91.29230 assigned negative charge : -364.4528 centred at (gu) : 91.39751 87.39313 91.16107 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6259 nv = 96 ne = 84 npr = 48610 no. pairs analyzed = 48610 no. exposed pairs = 3209 no. arc points = 23514 no. surface atoms = 1081 nbur = 1392 mkacc time = 8.0000006E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 309 mr = 3225 m= 5 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 8.9999996E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 3314 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2302 ## 253 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 7570 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.6867781E-09 6.9272819E-09 midg,1,midg; midg,igrid,midg 7.9865670E-09 -2.8971392E-09 1,midg,midg; igrid,midg,midg 3.2718719E-10 -1.9453334E-09 gauss-seidel spectral radius is 0.9860053 estimated iterations to convergence 69 setup time was (sec) 0.3800000 now iterating at: 03:20:05 rms-change max change #iterations 0.1122677 18.07269 at 10iterations 9.8365117E-03 1.488335 at 20iterations 8.5062167E-04 0.1203766 at 30iterations 7.3678209E-05 1.2096405E-02 at 40iterations 6.4690680E-06 1.1219978E-03 at 50iterations finished qdiffx linear iterations at : 03:20:08 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 6.4690680E-06 1.1219978E-03 energy calculations done at 3.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.400000 DelPhi exited at 03:20:09 3.404u 0.175s 0:03.92 91.0% 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 Tue Oct 11 2011 at 03:20:09 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 = 2473 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.824612 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): -37.45700 11.88900 ymin,ymax (A): -53.03400 1.908000 zmin,zma (A): -55.77600 2.757000 x,y,z range (A): 49.34600 54.94200 58.53300 scale (grids/A): 1.824612 object centre (A): -12.78400 -25.56300 -26.50950 number of atom coordinates read : 2473 total number of charged atoms : 2326 net assigned charge : -0.4999910 assigned positive charge : 363.9521 centred at (gu) : 94.12753 81.84917 93.87650 assigned negative charge : -364.4528 centred at (gu) : 94.19244 82.17933 93.48294 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 67701 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23514 grid for indexing accessible points = 1.400000 m= 23057 mr = 44958 m= 3308 mr = 16627 m= 149 mr = 1981 m= 0 mr = 21 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 30628 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 187 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 18186 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) : 0.6082039 object centre at (A) : -12.78400 -25.56300 -26.50950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.7142116E-02 6.3461242E-03 midg,1,midg; midg,igrid,midg 2.7033595E-02 -8.1221042E-03 1,midg,midg; igrid,midg,midg 2.9350026E-03 5.4884865E-04 gauss-seidel spectral radius is 0.9985045 estimated iterations to convergence 205 setup time was (sec) 0.5500000 now iterating at: 03:20:09 rms-change max change #iterations 3.711720 166.4151 at 10iterations 1.671598 64.86094 at 20iterations 0.7506649 25.01126 at 30iterations 0.3403510 11.98470 at 40iterations 0.1534396 5.067001 at 50iterations 6.9256447E-02 2.431250 at 60iterations 3.1064512E-02 1.066978 at 70iterations 1.4077958E-02 0.5132113 at 80iterations 6.3774814E-03 0.2260876 at 90iterations 2.8715439E-03 9.5632553E-02 at 100iterations 1.2947225E-03 4.3074608E-02 at 110iterations 5.8370660E-04 1.9906044E-02 at 120iterations finished qdiffx linear iterations at : 03:20:16 total time elapsed so far: 7.520000 # loops : 120 mean,max change (kT/e) : 5.8370660E-04 1.9906044E-02 energy calculations done at 7.520000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.660000 DelPhi exited at 03:20:17 7.659u 0.182s 0:08.28 94.5% 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 Tue Oct 11 2011 at 03:20:17 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 = 2473 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.736918 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): -37.45700 11.88900 ymin,ymax (A): -53.03400 1.908000 zmin,zma (A): -55.77600 2.757000 x,y,z range (A): 49.34600 54.94200 58.53300 scale (grids/A): 2.736918 object centre (A): -12.78400 -25.56300 -26.50950 number of atom coordinates read : 2473 total number of charged atoms : 2326 net assigned charge : -0.4999910 assigned positive charge : 363.9521 centred at (gu) : 96.19128 77.77367 95.81471 assigned negative charge : -364.4528 centred at (gu) : 96.28861 78.26889 95.22439 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 156264 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23514 grid for indexing accessible points = 1.400000 m= 75557 mr = 109170 m= 26443 mr = 60759 m= 5754 mr = 20992 m= 601 mr = 4171 m= 24 mr = 313 m= 0 mr = 5 time to grow re-entrant surface = 0.4600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8300000 number of dielectric boundary points 69233 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 0.9300000 number of grid points assigned charge 18607 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) : 1.824612 object centre at (A) : -12.78400 -25.56300 -26.50950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.7948787 0.1060524 midg,1,midg; midg,igrid,midg 0.2568494 -7.3865645E-02 1,midg,midg; igrid,midg,midg 5.6021728E-02 -9.5947934E-03 gauss-seidel spectral radius is 0.9992252 estimated iterations to convergence 284 setup time was (sec) 1.080000 now iterating at: 03:20:18 rms-change max change #iterations 8.985939 301.4056 at 10iterations 5.189681 119.7957 at 20iterations 2.959809 65.12398 at 30iterations 1.683574 35.80113 at 40iterations 0.9562898 18.58547 at 50iterations 0.5431119 17.12227 at 60iterations 0.3081528 5.989134 at 70iterations 0.1750883 3.417210 at 80iterations 9.8913297E-02 1.882509 at 90iterations 5.6016658E-02 1.108105 at 100iterations 3.1790510E-02 0.6061058 at 110iterations 1.8014196E-02 0.3615332 at 120iterations 1.0189511E-02 0.1890030 at 130iterations 5.7652937E-03 0.1196289 at 140iterations 3.2731213E-03 6.2231064E-02 at 150iterations 1.8526212E-03 3.3699036E-02 at 160iterations 1.0482484E-03 1.9866943E-02 at 170iterations 5.9378752E-04 1.1898041E-02 at 180iterations finished qdiffx linear iterations at : 03:20:30 total time elapsed so far: 12.26000 # loops : 180 mean,max change (kT/e) : 5.9378752E-04 1.1898041E-02 energy calculations done at 12.26000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.38000 DelPhi exited at 03:20:30 12.385u 0.207s 0:13.11 95.9% 0+0k 0+0io 0pf+0w