Tue Oct 11 03:34:56 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 03:34:56 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 = 2216 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: 0.6066079 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): 20.75100 70.84900 ymin,ymax (A): -15.72000 33.65300 zmin,zma (A): -9.669001 49.01800 x,y,z range (A): 50.09800 49.37300 58.68700 scale (grids/A): 0.6066079 object centre (A): 45.80000 8.966500 19.67450 number of atom coordinates read : 2216 total number of charged atoms : 2116 net assigned charge : -4.499984 assigned positive charge : 327.3584 centred at (gu) : 90.63865 89.43771 90.63864 assigned negative charge : -331.8588 centred at (gu) : 90.56873 89.59596 90.66218 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 5437 nv = 96 ne = 84 npr = 45409 no. pairs analyzed = 45409 no. exposed pairs = 2837 no. arc points = 20396 no. surface atoms = 957 nbur = 1259 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 263 mr = 2794 m= 2 mr = 19 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 8 time to turn everything in is 0.2600000 number of dielectric boundary points 2889 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1982 ## 168 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 6726 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.3392627E-09 -3.8351335E-09 midg,1,midg; midg,igrid,midg 4.0092782E-09 -7.5624307E-09 1,midg,midg; igrid,midg,midg -4.4412287E-09 2.7713634E-10 gauss-seidel spectral radius is 0.9859046 estimated iterations to convergence 69 setup time was (sec) 0.4900000 now iterating at: 03:34:57 rms-change max change #iterations 0.1020276 16.15982 at 10iterations 8.9760525E-03 1.411442 at 20iterations 7.9064060E-04 0.1236148 at 30iterations 6.8265821E-05 1.1581421E-02 at 40iterations 5.8785645E-06 9.3650818E-04 at 50iterations finished qdiffx linear iterations at : 03:34:59 total time elapsed so far: 3.160000 # loops : 50 mean,max change (kT/e) : 5.8785645E-06 9.3650818E-04 energy calculations done at 3.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.330000 DelPhi exited at 03:35:00 3.333u 0.221s 0:04.07 87.2% 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 03:35:00 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 = 2216 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: 1.819824 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): 20.75100 70.84900 ymin,ymax (A): -15.72000 33.65300 zmin,zma (A): -9.669001 49.01800 x,y,z range (A): 50.09800 49.37300 58.68700 scale (grids/A): 1.819824 object centre (A): 45.80000 8.966500 19.67450 number of atom coordinates read : 2216 total number of charged atoms : 2116 net assigned charge : -4.499984 assigned positive charge : 327.3584 centred at (gu) : 91.91568 88.31300 91.91568 assigned negative charge : -331.8588 centred at (gu) : 91.70611 88.78777 91.98648 start vw surface at 0.1600000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 58752 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20396 grid for indexing accessible points = 1.400000 m= 19704 mr = 39183 m= 2918 mr = 13922 m= 131 mr = 1668 m= 1 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 50 time to turn everything in is 0.4500000 number of dielectric boundary points 26699 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 131 iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 16552 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) : 0.6066079 object centre at (A) : 45.80000 8.966500 19.67450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.2212489E-02 1.8293884E-03 midg,1,midg; midg,igrid,midg 1.8519809E-02 -2.3006158E-02 1,midg,midg; igrid,midg,midg -1.2242650E-02 1.2790575E-03 gauss-seidel spectral radius is 0.9984732 estimated iterations to convergence 203 setup time was (sec) 0.7400000 now iterating at: 03:35:01 rms-change max change #iterations 3.497853 167.0575 at 10iterations 1.564001 59.15573 at 20iterations 0.7017602 27.97636 at 30iterations 0.3134533 11.62960 at 40iterations 0.1405416 5.795647 at 50iterations 6.2630437E-02 2.325169 at 60iterations 2.8082989E-02 1.029438 at 70iterations 1.2568200E-02 0.4608154 at 80iterations 5.6301453E-03 0.2185230 at 90iterations 2.5183670E-03 9.1050148E-02 at 100iterations 1.1313817E-03 4.0839195E-02 at 110iterations 5.0510094E-04 1.8905640E-02 at 120iterations finished qdiffx linear iterations at : 03:35:07 total time elapsed so far: 7.210000 # loops : 120 mean,max change (kT/e) : 5.0510094E-04 1.8905640E-02 energy calculations done at 7.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.390000 DelPhi exited at 03:35:08 7.397u 0.223s 0:07.93 95.9% 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 03:35:08 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2216 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: 2.729736 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): 20.75100 70.84900 ymin,ymax (A): -15.72000 33.65300 zmin,zma (A): -9.669001 49.01800 x,y,z range (A): 50.09800 49.37300 58.68700 scale (grids/A): 2.729736 object centre (A): 45.80000 8.966500 19.67450 number of atom coordinates read : 2216 total number of charged atoms : 2116 net assigned charge : -4.499984 assigned positive charge : 327.3584 centred at (gu) : 92.87346 87.46935 92.87342 assigned negative charge : -331.8588 centred at (gu) : 92.55921 88.18160 92.97963 start vw surface at 0.1900000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 135920 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20396 grid for indexing accessible points = 1.400000 m= 64246 mr = 95402 m= 22634 mr = 51244 m= 5017 mr = 17567 m= 523 mr = 3614 m= 21 mr = 316 m= 0 mr = 4 time to grow re-entrant surface = 0.5700001 no. cavity mid-points inaccessible to solvent = 154 time to turn everything in is 1.090000 number of dielectric boundary points 60214 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.200000 number of grid points assigned charge 16925 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) : 1.819824 object centre at (A) : 45.80000 8.966500 19.67450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3543765 9.3723617E-02 midg,1,midg; midg,igrid,midg 0.3368696 -0.2428001 1,midg,midg; igrid,midg,midg -7.0364431E-02 6.2891401E-02 gauss-seidel spectral radius is 0.9992099 estimated iterations to convergence 281 setup time was (sec) 1.370000 now iterating at: 03:35:10 rms-change max change #iterations 8.367506 282.0406 at 10iterations 4.744962 111.0420 at 20iterations 2.674006 55.90912 at 30iterations 1.504992 33.40261 at 40iterations 0.8480496 18.48689 at 50iterations 0.4780245 9.742405 at 60iterations 0.2678499 5.732712 at 70iterations 0.1508528 3.316193 at 80iterations 8.4576823E-02 1.694731 at 90iterations 4.7558475E-02 0.9452224 at 100iterations 2.6744058E-02 0.5780220 at 110iterations 1.5059020E-02 0.2952387 at 120iterations 8.4717097E-03 0.1797528 at 130iterations 4.7653411E-03 9.3681335E-02 at 140iterations 2.6746439E-03 5.7043076E-02 at 150iterations 1.5074738E-03 3.1898499E-02 at 160iterations 8.4853818E-04 1.7889023E-02 at 170iterations 4.7571262E-04 9.5748901E-03 at 180iterations finished qdiffx linear iterations at : 03:35:20 total time elapsed so far: 11.42000 # loops : 180 mean,max change (kT/e) : 4.7571262E-04 9.5748901E-03 energy calculations done at 11.42000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.59000 DelPhi exited at 03:35:20 11.594u 0.208s 0:12.12 97.2% 0+0k 0+0io 0pf+0w