Sat Oct 8 11:43:04 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 Sat Oct 8 2011 at 11:43:04 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: 321 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3372 !!! WARNING: HIR 694 has a net charge of 0.5140 !!! WARNING: HIR 698 has a net charge of 0.5140 !!! WARNING: HIR 704 has a net charge of 0.5140 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: 0.5509385 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): -4.293000 52.22400 ymin,ymax (A): 32.21700 95.55500 zmin,zma (A): -23.02900 41.58800 x,y,z range (A): 56.51700 63.33800 64.61700 scale (grids/A): 0.5509385 object centre (A): 23.96550 63.88600 9.279500 number of atom coordinates read : 3372 total number of charged atoms : 3221 net assigned charge : 3.542014 assigned positive charge : 532.5036 centred at (gu) : 90.60899 87.42923 89.75835 assigned negative charge : -528.9627 centred at (gu) : 90.74433 87.39437 89.67718 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 6737 nv = 96 ne = 84 npr = 63490 no. pairs analyzed = 63490 no. exposed pairs = 4585 no. arc points = 34269 no. surface atoms = 1533 nbur = 1839 mkacc time = 0.1100000 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= 262 mr = 3070 m= 1 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2500000 number of dielectric boundary points 3919 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3586 ## 539 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 8796 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.1641130E-10 9.8283226E-10 midg,1,midg; midg,igrid,midg -9.8162152E-11 3.3017947E-10 1,midg,midg; igrid,midg,midg 1.3247647E-09 -1.1780976E-09 gauss-seidel spectral radius is 0.9830576 estimated iterations to convergence 63 setup time was (sec) 0.4500000 now iterating at: 11:43:05 rms-change max change #iterations 8.0965012E-02 12.56555 at 10iterations 5.5451049E-03 0.8096924 at 20iterations 3.7983997E-04 5.7540894E-02 at 30iterations 2.5970859E-05 4.0397644E-03 at 40iterations 1.7387955E-06 2.4986267E-04 at 50iterations finished qdiffx linear iterations at : 11:43:08 total time elapsed so far: 3.460000 # loops : 50 mean,max change (kT/e) : 1.7387955E-06 2.4986267E-04 energy calculations done at 3.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.590000 DelPhi exited at 11:43:08 3.590u 0.186s 0:04.09 92.1% 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 Sat Oct 8 2011 at 11:43:08 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: 321 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3372 !!! WARNING: HIR 694 has a net charge of 0.5140 !!! WARNING: HIR 698 has a net charge of 0.5140 !!! WARNING: HIR 704 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.652816 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): -4.293000 52.22400 ymin,ymax (A): 32.21700 95.55500 zmin,zma (A): -23.02900 41.58800 x,y,z range (A): 56.51700 63.33800 64.61700 scale (grids/A): 1.652816 object centre (A): 23.96550 63.88600 9.279500 number of atom coordinates read : 3372 total number of charged atoms : 3221 net assigned charge : 3.542014 assigned positive charge : 532.5036 centred at (gu) : 91.82594 82.28690 89.27413 assigned negative charge : -528.9627 centred at (gu) : 92.23268 82.18267 89.03107 start vw surface at 0.1000000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 73439 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34269 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 20801 mr = 45832 m= 2244 mr = 13334 m= 60 mr = 1092 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 2258 time to turn everything in is 0.3700000 number of dielectric boundary points 36281 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 437 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 24697 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) : 0.5509385 object centre at (A) : 23.96550 63.88600 9.279500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.7142331E-02 9.7366860E-03 midg,1,midg; midg,igrid,midg 1.2817902E-02 9.4214100E-03 1,midg,midg; igrid,midg,midg 7.2414391E-03 -3.7585399E-03 gauss-seidel spectral radius is 0.9982797 estimated iterations to convergence 191 setup time was (sec) 0.6100000 now iterating at: 11:43:09 rms-change max change #iterations 3.720335 147.0203 at 10iterations 1.577904 55.67017 at 20iterations 0.6698737 22.63748 at 30iterations 0.2858450 10.70534 at 40iterations 0.1213017 4.041821 at 50iterations 5.1523551E-02 1.698090 at 60iterations 2.1906309E-02 0.7294865 at 70iterations 9.3594044E-03 0.3182583 at 80iterations 3.9817658E-03 0.1406240 at 90iterations 1.6965158E-03 5.6463242E-02 at 100iterations 7.2563911E-04 2.5731087E-02 at 110iterations 3.0752356E-04 1.0419846E-02 at 120iterations finished qdiffx linear iterations at : 11:43:17 total time elapsed so far: 8.130000 # loops : 120 mean,max change (kT/e) : 3.0752356E-04 1.0419846E-02 energy calculations done at 8.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.260000 DelPhi exited at 11:43:17 8.266u 0.216s 0:08.84 95.8% 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 Sat Oct 8 2011 at 11:43:17 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: 321 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3372 !!! WARNING: HIR 694 has a net charge of 0.5140 !!! WARNING: HIR 698 has a net charge of 0.5140 !!! WARNING: HIR 704 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.479223 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): -4.293000 52.22400 ymin,ymax (A): 32.21700 95.55500 zmin,zma (A): -23.02900 41.58800 x,y,z range (A): 56.51700 63.33800 64.61700 scale (grids/A): 2.479223 object centre (A): 23.96550 63.88600 9.279500 number of atom coordinates read : 3372 total number of charged atoms : 3221 net assigned charge : 3.542014 assigned positive charge : 532.5036 centred at (gu) : 92.73862 78.43010 88.91095 assigned negative charge : -528.9627 centred at (gu) : 93.34899 78.27399 88.54642 start vw surface at 0.1000000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 170405 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34269 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 72052 mr = 113176 m= 20028 mr = 54621 m= 3480 mr = 14301 m= 308 mr = 2263 m= 5 mr = 160 m= 0 mr = 0 time to grow re-entrant surface = 0.4700000 no. cavity mid-points inaccessible to solvent = 7648 time to turn everything in is 0.8800000 number of dielectric boundary points 81757 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 35 iepsmp to db, and charging done at 0.9800000 number of grid points assigned charge 25730 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) : 1.652816 object centre at (A) : 23.96550 63.88600 9.279500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3326650 2.7665304E-02 midg,1,midg; midg,igrid,midg 0.1243837 3.6271647E-02 1,midg,midg; igrid,midg,midg 6.5128475E-02 -5.9303656E-02 gauss-seidel spectral radius is 0.9991833 estimated iterations to convergence 276 setup time was (sec) 1.130000 now iterating at: 11:43:18 rms-change max change #iterations 9.812363 325.4543 at 10iterations 5.603889 137.7828 at 20iterations 3.182076 74.10918 at 30iterations 1.802161 40.08600 at 40iterations 1.016695 21.84504 at 50iterations 0.5730497 12.57926 at 60iterations 0.3212100 6.093744 at 70iterations 0.1805300 3.886655 at 80iterations 0.1009707 2.268849 at 90iterations 5.6501735E-02 1.245203 at 100iterations 3.1629693E-02 0.6040921 at 110iterations 1.7615788E-02 0.3789604 at 120iterations 9.8655391E-03 0.2028160 at 130iterations 5.5003953E-03 0.1047487 at 140iterations 3.0820274E-03 5.5983067E-02 at 150iterations 1.7203684E-03 3.2497406E-02 at 160iterations 9.5888844E-04 1.9752502E-02 at 170iterations 5.3532905E-04 1.0490417E-02 at 180iterations finished qdiffx linear iterations at : 11:43:30 total time elapsed so far: 13.07000 # loops : 180 mean,max change (kT/e) : 5.3532905E-04 1.0490417E-02 energy calculations done at 13.07000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.20000 DelPhi exited at 11:43:31 13.201u 0.234s 0:13.76 97.6% 0+0k 0+0io 0pf+0w