Mon Oct 10 21:09:15 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 21:09:15 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 = 2712 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: 0.6148532 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): -9.999000 45.71300 ymin,ymax (A): 32.14800 85.59200 zmin,zma (A): -11.55400 46.34600 x,y,z range (A): 55.71200 53.44400 57.90000 scale (grids/A): 0.6148532 object centre (A): 17.85700 58.87000 17.39600 number of atom coordinates read : 2712 total number of charged atoms : 2575 net assigned charge : 1.500006 assigned positive charge : 401.5747 centred at (gu) : 89.30818 88.80894 89.64435 assigned negative charge : -400.0758 centred at (gu) : 89.28780 88.78951 89.65379 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7032 nv = 96 ne = 84 npr = 52984 no. pairs analyzed = 52984 no. exposed pairs = 3961 no. arc points = 28440 no. surface atoms = 1303 nbur = 1409 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 394 mr = 3328 m= 5 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 4083 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2682 ## 228 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 8417 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.7354260E-09 4.6054224E-10 midg,1,midg; midg,igrid,midg -1.4466771E-10 1.6884101E-09 1,midg,midg; igrid,midg,midg -1.8730618E-10 1.9300475E-09 gauss-seidel spectral radius is 0.9863307 estimated iterations to convergence 70 setup time was (sec) 0.3900000 now iterating at: 21:09:16 rms-change max change #iterations 0.1222422 20.51995 at 10iterations 1.0914587E-02 1.514252 at 20iterations 1.0218800E-03 0.1548691 at 30iterations 1.1829391E-04 1.7578125E-02 at 40iterations 2.3080300E-05 3.0522346E-03 at 50iterations finished qdiffx linear iterations at : 21:09:18 total time elapsed so far: 3.240000 # loops : 50 mean,max change (kT/e) : 2.3080300E-05 3.0522346E-03 energy calculations done at 3.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.370000 DelPhi exited at 21:09:19 3.374u 0.169s 0:04.03 87.5% 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 Mon Oct 10 2011 at 21:09:19 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 = 2712 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: 1.844560 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): -9.999000 45.71300 ymin,ymax (A): 32.14800 85.59200 zmin,zma (A): -11.55400 46.34600 x,y,z range (A): 55.71200 53.44400 57.90000 scale (grids/A): 1.844560 object centre (A): 17.85700 58.87000 17.39600 number of atom coordinates read : 2712 total number of charged atoms : 2575 net assigned charge : 1.500006 assigned positive charge : 401.5747 centred at (gu) : 87.92376 86.42644 88.93237 assigned negative charge : -400.0758 centred at (gu) : 87.86312 86.36848 88.96133 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 74489 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28440 grid for indexing accessible points = 1.400000 m= 26687 mr = 47381 m= 4385 mr = 18178 m= 248 mr = 2364 m= 1 mr = 48 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 37839 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 165 iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 20202 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) : 0.6148532 object centre at (A) : 17.85700 58.87000 17.39600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.8755518E-03 -1.3194097E-02 midg,1,midg; midg,igrid,midg 3.5331301E-02 1.6874300E-02 1,midg,midg; igrid,midg,midg -5.5514695E-03 -3.2474762E-03 gauss-seidel spectral radius is 0.9985849 estimated iterations to convergence 211 setup time was (sec) 0.5900000 now iterating at: 21:09:20 rms-change max change #iterations 4.048794 167.7650 at 10iterations 1.847964 65.16561 at 20iterations 0.8540658 27.56647 at 30iterations 0.3914006 12.58524 at 40iterations 0.1804198 5.976778 at 50iterations 8.2630970E-02 2.515250 at 60iterations 3.8175020E-02 1.196075 at 70iterations 1.7591270E-02 0.5655785 at 80iterations 8.1134290E-03 0.2674809 at 90iterations 3.7547492E-03 0.1378098 at 100iterations 1.7301509E-03 5.5992126E-02 at 110iterations 8.0190430E-04 2.3494244E-02 at 120iterations finished qdiffx linear iterations at : 21:09:27 total time elapsed so far: 7.650000 # loops : 120 mean,max change (kT/e) : 8.0190430E-04 2.3494244E-02 energy calculations done at 7.650000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.790000 DelPhi exited at 21:09:28 7.791u 0.201s 0:08.65 92.3% 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 21:09:28 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 = 2712 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.766839 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): -9.999000 45.71300 ymin,ymax (A): 32.14800 85.59200 zmin,zma (A): -11.55400 46.34600 x,y,z range (A): 55.71200 53.44400 57.90000 scale (grids/A): 2.766839 object centre (A): 17.85700 58.87000 17.39600 number of atom coordinates read : 2712 total number of charged atoms : 2575 net assigned charge : 1.500006 assigned positive charge : 401.5747 centred at (gu) : 86.88548 84.63942 88.39838 assigned negative charge : -400.0758 centred at (gu) : 86.79464 84.55257 88.44192 start vw surface at 0.1000000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 172097 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28440 grid for indexing accessible points = 1.400000 m= 83784 mr = 116328 m= 31344 mr = 64837 m= 7479 mr = 23645 m= 920 mr = 4982 m= 57 mr = 479 m= 1 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.5599999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9800000 number of dielectric boundary points 85398 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.070000 number of grid points assigned charge 20598 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) : 1.844560 object centre at (A) : 17.85700 58.87000 17.39600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.3373710E-02 -9.1701053E-02 midg,1,midg; midg,igrid,midg 0.5981359 0.2663198 1,midg,midg; igrid,midg,midg 6.3716002E-02 -4.1715089E-02 gauss-seidel spectral radius is 0.9992672 estimated iterations to convergence 292 setup time was (sec) 1.210000 now iterating at: 21:09:29 rms-change max change #iterations 10.02607 286.0839 at 10iterations 6.017966 179.4690 at 20iterations 3.571217 85.71059 at 30iterations 2.102296 44.07451 at 40iterations 1.232669 25.33149 at 50iterations 0.7207177 15.23225 at 60iterations 0.4195642 8.700911 at 70iterations 0.2434651 4.895373 at 80iterations 0.1412838 2.713459 at 90iterations 8.1757575E-02 1.513238 at 100iterations 4.7257297E-02 0.9542966 at 110iterations 2.7387090E-02 0.4997020 at 120iterations 1.5817057E-02 0.2976913 at 130iterations 9.1614844E-03 0.1893101 at 140iterations 5.2877213E-03 9.8601341E-02 at 150iterations 3.0532493E-03 5.8891296E-02 at 160iterations 1.7644466E-03 3.5241127E-02 at 170iterations 1.0232847E-03 1.9335747E-02 at 180iterations finished qdiffx linear iterations at : 21:09:41 total time elapsed so far: 12.77000 # loops : 180 mean,max change (kT/e) : 1.0232847E-03 1.9335747E-02 energy calculations done at 12.77000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.90000 DelPhi exited at 21:09:42 12.907u 0.216s 0:13.79 95.0% 0+0k 0+0io 0pf+0w