Tue Oct 11 05:58:02 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 05:58:02 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 = 2073 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7399709 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): -17.95700 30.15300 ymin,ymax (A): -11.47900 30.56100 zmin,zma (A): -8.546000 38.11900 x,y,z range (A): 48.11000 42.04000 46.66500 scale (grids/A): 0.7399709 object centre (A): 6.098001 9.541000 14.78650 number of atom coordinates read : 2073 total number of charged atoms : 1945 net assigned charge : 6.500009 assigned positive charge : 314.9840 centred at (gu) : 90.10739 89.69218 91.00662 assigned negative charge : -308.4842 centred at (gu) : 90.04530 89.60563 90.89044 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7808 nv = 96 ne = 84 npr = 41863 no. pairs analyzed = 41863 no. exposed pairs = 2536 no. arc points = 17150 no. surface atoms = 864 nbur = 1209 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 569 mr = 4569 m= 1 mr = 132 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 47 time to turn everything in is 0.1700000 number of dielectric boundary points 3677 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1538 ## 149 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 8240 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.7333162E-11 2.7267782E-07 midg,1,midg; midg,igrid,midg 2.9380084E-08 1.8652342E-07 1,midg,midg; igrid,midg,midg 5.1452012E-08 1.7733312E-07 gauss-seidel spectral radius is 0.9904717 estimated iterations to convergence 83 setup time was (sec) 0.3800000 now iterating at: 05:58:02 rms-change max change #iterations 0.2397702 30.46323 at 10iterations 3.2561123E-02 4.473305 at 20iterations 4.5673447E-03 0.6100979 at 30iterations 7.0717878E-04 9.9330425E-02 at 40iterations 1.4676388E-04 1.7074585E-02 at 50iterations finished qdiffx linear iterations at : 05:58:05 total time elapsed so far: 3.420000 # loops : 50 mean,max change (kT/e) : 1.4676388E-04 1.7074585E-02 energy calculations done at 3.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.560000 DelPhi exited at 05:58:06 3.562u 0.186s 0:04.10 91.2% 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 Tue Oct 11 2011 at 05:58:06 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 = 2073 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.219913 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): -17.95700 30.15300 ymin,ymax (A): -11.47900 30.56100 zmin,zma (A): -8.546000 38.11900 x,y,z range (A): 48.11000 42.04000 46.66500 scale (grids/A): 2.219913 object centre (A): 6.098001 9.541000 14.78650 number of atom coordinates read : 2073 total number of charged atoms : 1945 net assigned charge : 6.500009 assigned positive charge : 314.9840 centred at (gu) : 90.32217 89.07650 93.01988 assigned negative charge : -308.4842 centred at (gu) : 90.13605 88.81688 92.67137 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 81734 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17150 grid for indexing accessible points = 1.400000 m= 35076 mr = 58549 m= 7705 mr = 27335 m= 861 mr = 5429 m= 32 mr = 486 m= 0 mr = 8 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 1234 time to turn everything in is 0.4200000 number of dielectric boundary points 33601 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 55 iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 15490 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) : 0.7399709 object centre at (A) : 6.098001 9.541000 14.78650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.8572294E-02 4.8616726E-02 midg,1,midg; midg,igrid,midg 3.1956855E-02 3.0728493E-02 1,midg,midg; igrid,midg,midg 5.0706312E-02 3.7116542E-02 gauss-seidel spectral radius is 0.9989151 estimated iterations to convergence 240 setup time was (sec) 0.6600000 now iterating at: 05:58:07 rms-change max change #iterations 4.985627 180.2173 at 10iterations 2.528570 96.89441 at 20iterations 1.288815 38.87612 at 30iterations 0.6550325 18.66531 at 40iterations 0.3340415 10.85390 at 50iterations 0.1705033 4.888382 at 60iterations 8.6518362E-02 2.564655 at 70iterations 4.4257063E-02 1.220788 at 80iterations 2.2577297E-02 0.6271820 at 90iterations 1.1594202E-02 0.3209991 at 100iterations 5.9301672E-03 0.1639879 at 110iterations 3.0801825E-03 8.8237762E-02 at 120iterations finished qdiffx linear iterations at : 05:58:14 total time elapsed so far: 8.200000 # loops : 120 mean,max change (kT/e) : 3.0801825E-03 8.8237762E-02 energy calculations done at 8.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.340000 DelPhi exited at 05:58:15 8.340u 0.231s 0:08.95 95.7% 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 05:58:15 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2073 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.329869 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): -17.95700 30.15300 ymin,ymax (A): -11.47900 30.56100 zmin,zma (A): -8.546000 38.11900 x,y,z range (A): 48.11000 42.04000 46.66500 scale (grids/A): 3.329869 object centre (A): 6.098001 9.541000 14.78650 number of atom coordinates read : 2073 total number of charged atoms : 1945 net assigned charge : 6.500009 assigned positive charge : 314.9840 centred at (gu) : 90.48334 88.61463 94.52987 assigned negative charge : -308.4842 centred at (gu) : 90.20409 88.22529 94.00700 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 188171 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17150 grid for indexing accessible points = 1.400000 m= 106437 mr = 140683 m= 47033 mr = 89653 m= 14973 mr = 39470 m= 3348 mr = 12024 m= 511 mr = 2553 m= 34 mr = 367 m= 0 mr = 22 time to grow re-entrant surface = 0.6899999 no. cavity mid-points inaccessible to solvent = 4493 time to turn everything in is 1.320000 number of dielectric boundary points 75735 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.420000 number of grid points assigned charge 15560 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) : 2.219913 object centre at (A) : 6.098001 9.541000 14.78650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5385299 0.4463528 midg,1,midg; midg,igrid,midg 0.2811173 0.1550275 1,midg,midg; igrid,midg,midg 0.3151416 0.1555757 gauss-seidel spectral radius is 0.9993186 estimated iterations to convergence 302 setup time was (sec) 1.570000 now iterating at: 05:58:17 rms-change max change #iterations 10.80146 287.8182 at 10iterations 6.454158 143.3768 at 20iterations 3.840415 76.43305 at 30iterations 2.290674 40.53773 at 40iterations 1.360555 23.79585 at 50iterations 0.8063564 14.74811 at 60iterations 0.4775239 9.003058 at 70iterations 0.2826226 4.981283 at 80iterations 0.1669120 2.859365 at 90iterations 9.8862134E-02 1.697060 at 100iterations 5.8524590E-02 1.143574 at 110iterations 3.4686022E-02 0.5420122 at 120iterations 2.0613562E-02 0.3544846 at 130iterations 1.2406271E-02 0.2364578 at 140iterations 7.5738570E-03 0.1304131 at 150iterations 4.7515663E-03 8.4983826E-02 at 160iterations 3.1032786E-03 5.4986954E-02 at 170iterations 2.1497689E-03 3.7189484E-02 at 180iterations finished qdiffx linear iterations at : 05:58:29 total time elapsed so far: 13.66000 # loops : 180 mean,max change (kT/e) : 2.1497689E-03 3.7189484E-02 energy calculations done at 13.66000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.80000 DelPhi exited at 05:58:29 13.799u 0.241s 0:14.33 97.9% 0+0k 0+0io 0pf+0w