Sun Oct 9 16:14:43 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 Sun Oct 9 2011 at 16:14:43 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 = 3147 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6020021 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): -15.68300 37.54800 ymin,ymax (A): 3.265000 55.91900 zmin,zma (A): -34.57100 24.56500 x,y,z range (A): 53.23100 52.65400 59.13600 scale (grids/A): 0.6020021 object centre (A): 10.93250 29.59200 -5.002999 number of atom coordinates read : 3147 total number of charged atoms : 3003 net assigned charge : -5.499976 assigned positive charge : 466.8008 centred at (gu) : 89.96905 91.10933 88.21513 assigned negative charge : -472.3023 centred at (gu) : 90.01669 91.21968 88.15479 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7418 nv = 96 ne = 84 npr = 65266 no. pairs analyzed = 65266 no. exposed pairs = 3751 no. arc points = 26194 no. surface atoms = 1278 nbur = 1869 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 394 mr = 4097 m= 2 mr = 45 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 33 time to turn everything in is 0.3400000 number of dielectric boundary points 3672 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2645 ## 265 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 9429 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.8529014E-09 2.5691041E-10 midg,1,midg; midg,igrid,midg 2.1019064E-09 -9.8282955E-09 1,midg,midg; igrid,midg,midg -1.5147728E-10 -4.5964259E-09 gauss-seidel spectral radius is 0.9857611 estimated iterations to convergence 69 setup time was (sec) 0.5600000 now iterating at: 16:14:44 rms-change max change #iterations 0.1252137 17.99416 at 10iterations 1.0753639E-02 1.583313 at 20iterations 9.4922236E-04 0.1680832 at 30iterations 1.0822032E-04 1.8058300E-02 at 40iterations 2.5168058E-05 5.1174164E-03 at 50iterations finished qdiffx linear iterations at : 16:14:46 total time elapsed so far: 2.960000 # loops : 50 mean,max change (kT/e) : 2.5168058E-05 5.1174164E-03 energy calculations done at 2.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.120000 DelPhi exited at 16:14:46 3.127u 0.139s 0:03.57 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 Sun Oct 9 2011 at 16:14:46 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 = 3147 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: 1.806006 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): -15.68300 37.54800 ymin,ymax (A): 3.265000 55.91900 zmin,zma (A): -34.57100 24.56500 x,y,z range (A): 53.23100 52.65400 59.13600 scale (grids/A): 1.806006 object centre (A): 10.93250 29.59200 -5.002999 number of atom coordinates read : 3147 total number of charged atoms : 3003 net assigned charge : -5.499976 assigned positive charge : 466.8008 centred at (gu) : 89.90600 93.32704 84.64455 assigned negative charge : -472.3023 centred at (gu) : 90.04993 93.65858 84.46377 start vw surface at 0.1600000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 81832 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26194 grid for indexing accessible points = 1.400000 m= 28053 mr = 57375 m= 4195 mr = 20396 m= 218 mr = 2514 m= 2 mr = 61 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 602 time to turn everything in is 0.5600000 number of dielectric boundary points 33954 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 176 iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 23474 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) : 0.6020021 object centre at (A) : 10.93250 29.59200 -5.002999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.8830141E-03 2.2761375E-03 midg,1,midg; midg,igrid,midg -1.3253276E-02 -2.3398511E-02 1,midg,midg; igrid,midg,midg -2.2685209E-02 -1.8591342E-02 gauss-seidel spectral radius is 0.9985304 estimated iterations to convergence 207 setup time was (sec) 0.8300000 now iterating at: 16:14:47 rms-change max change #iterations 4.281617 170.7725 at 10iterations 1.938854 63.31549 at 20iterations 0.8808565 30.18605 at 30iterations 0.4014100 12.33382 at 40iterations 0.1824876 5.837458 at 50iterations 8.3143957E-02 2.584949 at 60iterations 3.7893850E-02 1.237546 at 70iterations 1.7260890E-02 0.5776062 at 80iterations 7.8650648E-03 0.2264652 at 90iterations 3.5780780E-03 0.1211376 at 100iterations 1.6404284E-03 4.6371460E-02 at 110iterations 7.4764277E-04 2.1612167E-02 at 120iterations finished qdiffx linear iterations at : 16:14:53 total time elapsed so far: 6.820000 # loops : 120 mean,max change (kT/e) : 7.4764277E-04 2.1612167E-02 energy calculations done at 6.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.990000 DelPhi exited at 16:14:54 6.991u 0.157s 0:07.41 96.3% 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 Sun Oct 9 2011 at 16:14:54 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 = 3147 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: 2.709010 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): -15.68300 37.54800 ymin,ymax (A): 3.265000 55.91900 zmin,zma (A): -34.57100 24.56500 x,y,z range (A): 53.23100 52.65400 59.13600 scale (grids/A): 2.709010 object centre (A): 10.93250 29.59200 -5.002999 number of atom coordinates read : 3147 total number of charged atoms : 3003 net assigned charge : -5.499976 assigned positive charge : 466.8008 centred at (gu) : 89.85876 94.99031 81.96655 assigned negative charge : -472.3023 centred at (gu) : 90.07480 95.48785 81.69564 start vw surface at 0.1400000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 190311 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26194 grid for indexing accessible points = 1.400000 m= 92495 mr = 140265 m= 32107 mr = 74969 m= 7345 mr = 25323 m= 913 mr = 5368 m= 39 mr = 552 m= 0 mr = 19 time to grow re-entrant surface = 0.8100000 no. cavity mid-points inaccessible to solvent = 2129 time to turn everything in is 1.370000 number of dielectric boundary points 76714 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.490000 number of grid points assigned charge 24024 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) : 1.806006 object centre at (A) : 10.93250 29.59200 -5.002999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.6791068E-02 0.1246095 midg,1,midg; midg,igrid,midg -0.2224141 -0.2533752 1,midg,midg; igrid,midg,midg -0.3503490 -0.2425033 gauss-seidel spectral radius is 0.9992388 estimated iterations to convergence 286 setup time was (sec) 1.650000 now iterating at: 16:14:56 rms-change max change #iterations 10.24613 317.3153 at 10iterations 5.963916 137.8162 at 20iterations 3.452037 69.51540 at 30iterations 1.983402 40.24213 at 40iterations 1.140958 23.35686 at 50iterations 0.6534417 16.60678 at 60iterations 0.3742405 6.983382 at 70iterations 0.2149291 3.854889 at 80iterations 0.1225971 2.499877 at 90iterations 7.0203841E-02 1.321870 at 100iterations 4.0176954E-02 0.8025789 at 110iterations 2.2911374E-02 0.4467225 at 120iterations 1.3092906E-02 0.2614174 at 130iterations 7.4704462E-03 0.1377945 at 140iterations 4.2590513E-03 8.3202362E-02 at 150iterations 2.4317028E-03 4.2579174E-02 at 160iterations 1.3869007E-03 2.3651123E-02 at 170iterations 7.9202070E-04 1.3454437E-02 at 180iterations finished qdiffx linear iterations at : 16:15:05 total time elapsed so far: 11.17000 # loops : 180 mean,max change (kT/e) : 7.9202070E-04 1.3454437E-02 energy calculations done at 11.17000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.35000 DelPhi exited at 16:15:06 11.352u 0.175s 0:11.79 97.7% 0+0k 0+0io 0pf+0w