Mon Oct 10 19:37:42 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 Mon Oct 10 2011 at 19:37:42 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2738 !!! WARNING: HIR 108 has a net charge of 0.5140 !!! WARNING: HIR 234 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: 0.6120309 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): -13.33300 37.44500 ymin,ymax (A): -35.48400 22.68300 zmin,zma (A): 4.138000 61.49500 x,y,z range (A): 50.77800 58.16700 57.35700 scale (grids/A): 0.6120309 object centre (A): 12.05600 -6.400500 32.81650 number of atom coordinates read : 2738 total number of charged atoms : 2600 net assigned charge : 8.528040 assigned positive charge : 405.6915 centred at (gu) : 90.94991 92.78181 89.09081 assigned negative charge : -397.1648 centred at (gu) : 91.01157 92.84145 89.11600 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6965 nv = 96 ne = 84 npr = 54418 no. pairs analyzed = 54418 no. exposed pairs = 3741 no. arc points = 26043 no. surface atoms = 1263 nbur = 1475 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 390 mr = 3545 m= 1 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3765 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2627 ## 251 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 8498 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.2565048E-09 3.3735070E-09 midg,1,midg; midg,igrid,midg 4.7027706E-09 3.9149861E-09 1,midg,midg; igrid,midg,midg 7.0579773E-09 2.5671971E-09 gauss-seidel spectral radius is 0.9861988 estimated iterations to convergence 70 setup time was (sec) 0.6300000 now iterating at: 19:37:43 rms-change max change #iterations 0.1238279 18.49736 at 10iterations 1.1109750E-02 1.717823 at 20iterations 1.1122462E-03 0.1825104 at 30iterations 1.5702882E-04 2.8184891E-02 at 40iterations 3.2681372E-05 6.7520142E-03 at 50iterations finished qdiffx linear iterations at : 19:37:47 total time elapsed so far: 4.710000 # loops : 50 mean,max change (kT/e) : 3.2681372E-05 6.7520142E-03 energy calculations done at 4.710000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.880000 DelPhi exited at 19:37:48 4.886u 0.387s 0:05.85 89.9% 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 Mon Oct 10 2011 at 19:37:48 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2738 !!! WARNING: HIR 108 has a net charge of 0.5140 !!! WARNING: HIR 234 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: 1.836093 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): -13.33300 37.44500 ymin,ymax (A): -35.48400 22.68300 zmin,zma (A): 4.138000 61.49500 x,y,z range (A): 50.77800 58.16700 57.35700 scale (grids/A): 1.836093 object centre (A): 12.05600 -6.400500 32.81650 number of atom coordinates read : 2738 total number of charged atoms : 2600 net assigned charge : 8.528040 assigned positive charge : 405.6915 centred at (gu) : 92.84901 98.34483 87.27185 assigned negative charge : -397.1648 centred at (gu) : 93.03458 98.52439 87.34776 start vw surface at 0.1300000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 74957 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26043 grid for indexing accessible points = 1.400000 m= 26275 mr = 50078 m= 4193 mr = 18417 m= 204 mr = 2489 m= 2 mr = 45 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 495 time to turn everything in is 0.6400000 number of dielectric boundary points 34602 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 169 iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 20377 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) : 0.6120309 object centre at (A) : 12.05600 -6.400500 32.81650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.4752163E-03 1.3677372E-02 midg,1,midg; midg,igrid,midg 3.0534128E-02 4.6548817E-02 1,midg,midg; igrid,midg,midg 1.5880739E-02 1.4918327E-02 gauss-seidel spectral radius is 0.9985543 estimated iterations to convergence 209 setup time was (sec) 0.9400000 now iterating at: 19:37:49 rms-change max change #iterations 4.030786 154.1396 at 10iterations 1.838346 75.46198 at 20iterations 0.8422099 27.08033 at 30iterations 0.3858807 13.55291 at 40iterations 0.1764009 5.666023 at 50iterations 8.0630556E-02 2.584324 at 60iterations 3.7047449E-02 1.193649 at 70iterations 1.6922256E-02 0.5398808 at 80iterations 7.7825254E-03 0.2534790 at 90iterations 3.5801902E-03 0.1142225 at 100iterations 1.6516362E-03 5.8031082E-02 at 110iterations 7.6604699E-04 2.4471283E-02 at 120iterations finished qdiffx linear iterations at : 19:38:00 total time elapsed so far: 11.79000 # loops : 120 mean,max change (kT/e) : 7.6604699E-04 2.4471283E-02 energy calculations done at 11.79000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.96000 DelPhi exited at 19:38:00 11.966u 0.438s 0:12.69 97.6% 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 19:38:00 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2738 !!! WARNING: HIR 108 has a net charge of 0.5140 !!! WARNING: HIR 234 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: 2.754139 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): -13.33300 37.44500 ymin,ymax (A): -35.48400 22.68300 zmin,zma (A): 4.138000 61.49500 x,y,z range (A): 50.77800 58.16700 57.35700 scale (grids/A): 2.754139 object centre (A): 12.05600 -6.400500 32.81650 number of atom coordinates read : 2738 total number of charged atoms : 2600 net assigned charge : 8.528040 assigned positive charge : 405.6915 centred at (gu) : 94.27341 102.5169 85.90778 assigned negative charge : -397.1648 centred at (gu) : 94.55187 102.7866 86.02175 start vw surface at 0.1200000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 173380 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26043 grid for indexing accessible points = 1.400000 m= 84282 mr = 122024 m= 30671 mr = 66560 m= 7519 mr = 24035 m= 945 mr = 5445 m= 44 mr = 569 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.9800001 no. cavity mid-points inaccessible to solvent = 1453 time to turn everything in is 1.610000 number of dielectric boundary points 78199 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.740000 number of grid points assigned charge 20798 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) : 1.836093 object centre at (A) : 12.05600 -6.400500 32.81650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.5551460E-02 0.1887506 midg,1,midg; midg,igrid,midg 0.3308096 0.8285374 1,midg,midg; igrid,midg,midg 0.1404835 0.2317404 gauss-seidel spectral radius is 0.9992520 estimated iterations to convergence 289 setup time was (sec) 1.940000 now iterating at: 19:38:03 rms-change max change #iterations 9.925837 313.0846 at 10iterations 5.896518 129.2984 at 20iterations 3.458850 75.93094 at 30iterations 2.022484 43.14585 at 40iterations 1.176981 24.48071 at 50iterations 0.6829200 17.83806 at 60iterations 0.3942605 8.564056 at 70iterations 0.2281228 4.471521 at 80iterations 0.1313501 2.811815 at 90iterations 7.5711854E-02 1.699612 at 100iterations 4.3531921E-02 0.8568792 at 110iterations 2.5088806E-02 0.4817467 at 120iterations 1.4411479E-02 0.2891655 at 130iterations 8.3079487E-03 0.1756287 at 140iterations 4.7849854E-03 0.1127014 at 150iterations 2.7668010E-03 5.4101944E-02 at 160iterations 1.6119650E-03 3.6077738E-02 at 170iterations 9.4588572E-04 1.8173218E-02 at 180iterations finished qdiffx linear iterations at : 19:38:20 total time elapsed so far: 19.39000 # loops : 180 mean,max change (kT/e) : 9.4588572E-04 1.8173218E-02 energy calculations done at 19.39000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.56000 DelPhi exited at 19:38:21 19.563u 0.459s 0:20.55 97.3% 0+0k 0+0io 0pf+0w