Sun Oct 9 12:42:02 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 Sun Oct 9 2011 at 12:42:02 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 = 2385 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6760607 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): -7.672000 44.24500 ymin,ymax (A): -14.21800 38.44000 zmin,zma (A): 1.100000 44.40900 x,y,z range (A): 51.91700 52.65800 43.30900 scale (grids/A): 0.6760607 object centre (A): 18.28650 12.11100 22.75450 number of atom coordinates read : 2385 total number of charged atoms : 2243 net assigned charge : 2.500025 assigned positive charge : 362.6770 centred at (gu) : 90.03014 90.71450 91.17937 assigned negative charge : -360.1776 centred at (gu) : 90.04736 90.90395 91.23444 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7281 nv = 96 ne = 84 npr = 48238 no. pairs analyzed = 48238 no. exposed pairs = 2936 no. arc points = 21080 no. surface atoms = 992 nbur = 1393 mkacc time = 8.0000006E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 414 mr = 3999 m= 2 mr = 62 m= 0 mr = 0 time to grow re-entrant surface = 8.9999996E-02 no. cavity mid-points inaccessible to solvent = 63 time to turn everything in is 0.1900000 number of dielectric boundary points 3636 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2066 ## 210 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 8483 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.9994818E-08 -6.3105405E-09 midg,1,midg; midg,igrid,midg 5.2905786E-08 -4.9494652E-08 1,midg,midg; igrid,midg,midg 1.4990013E-08 5.6862453E-09 gauss-seidel spectral radius is 0.9886369 estimated iterations to convergence 77 setup time was (sec) 0.3800000 now iterating at: 12:42:03 rms-change max change #iterations 0.1773247 29.59180 at 10iterations 2.0229492E-02 2.818616 at 20iterations 2.7226517E-03 0.3947906 at 30iterations 5.9536466E-04 9.2950821E-02 at 40iterations 1.9435324E-04 3.1766891E-02 at 50iterations finished qdiffx linear iterations at : 12:42:05 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 1.9435324E-04 3.1766891E-02 energy calculations done at 3.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 12:42:06 3.391u 0.168s 0:03.89 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 Sun Oct 9 2011 at 12:42:06 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 = 2385 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.028182 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): -7.672000 44.24500 ymin,ymax (A): -14.21800 38.44000 zmin,zma (A): 1.100000 44.40900 x,y,z range (A): 51.91700 52.65800 43.30900 scale (grids/A): 2.028182 object centre (A): 18.28650 12.11100 22.75450 number of atom coordinates read : 2385 total number of charged atoms : 2243 net assigned charge : 2.500025 assigned positive charge : 362.6770 centred at (gu) : 90.09019 92.14297 93.53771 assigned negative charge : -360.1776 centred at (gu) : 90.14187 92.71148 93.70325 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 77756 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21080 grid for indexing accessible points = 1.400000 m= 29533 mr = 53722 m= 5007 mr = 22068 m= 406 mr = 3222 m= 7 mr = 213 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 2293 time to turn everything in is 0.3900000 number of dielectric boundary points 33484 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 138 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 17749 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) : 0.6760607 object centre at (A) : 18.28650 12.11100 22.75450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.6531705E-02 6.6016023E-03 midg,1,midg; midg,igrid,midg 1.9135553E-02 -6.3636541E-02 1,midg,midg; igrid,midg,midg 4.0457189E-02 -1.0588658E-02 gauss-seidel spectral radius is 0.9987714 estimated iterations to convergence 226 setup time was (sec) 0.6100000 now iterating at: 12:42:07 rms-change max change #iterations 4.582493 206.7458 at 10iterations 2.219577 74.29211 at 20iterations 1.081846 35.26249 at 30iterations 0.5290449 16.96119 at 40iterations 0.2565922 8.711143 at 50iterations 0.1250260 3.899350 at 60iterations 6.1116617E-02 1.876038 at 70iterations 2.9878134E-02 0.9258556 at 80iterations 1.4699461E-02 0.4307938 at 90iterations 7.2949803E-03 0.2308769 at 100iterations 3.6809517E-03 0.1292992 at 110iterations 1.9122824E-03 5.7972431E-02 at 120iterations finished qdiffx linear iterations at : 12:42:14 total time elapsed so far: 7.800000 # loops : 120 mean,max change (kT/e) : 1.9122824E-03 5.7972431E-02 energy calculations done at 7.800000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.930000 DelPhi exited at 12:42:14 7.937u 0.195s 0:08.46 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 Sun Oct 9 2011 at 12:42:14 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 = 2385 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.042273 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): -7.672000 44.24500 ymin,ymax (A): -14.21800 38.44000 zmin,zma (A): 1.100000 44.40900 x,y,z range (A): 51.91700 52.65800 43.30900 scale (grids/A): 3.042273 object centre (A): 18.28650 12.11100 22.75450 number of atom coordinates read : 2385 total number of charged atoms : 2243 net assigned charge : 2.500025 assigned positive charge : 362.6770 centred at (gu) : 90.13522 93.21434 95.30650 assigned negative charge : -360.1776 centred at (gu) : 90.21270 94.06719 95.55482 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 179228 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21080 grid for indexing accessible points = 1.400000 m= 93919 mr = 129691 m= 35733 mr = 77380 m= 9141 mr = 28978 m= 1664 mr = 7020 m= 152 mr = 1233 m= 0 mr = 94 time to grow re-entrant surface = 0.5800000 no. cavity mid-points inaccessible to solvent = 7902 time to turn everything in is 1.000000 number of dielectric boundary points 75441 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.090000 number of grid points assigned charge 17943 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) : 2.028182 object centre at (A) : 18.28650 12.11100 22.75450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3618132 -3.8054951E-02 midg,1,midg; midg,igrid,midg 0.4602425 -0.6244188 1,midg,midg; igrid,midg,midg 0.3741357 -0.4009694 gauss-seidel spectral radius is 0.9992830 estimated iterations to convergence 295 setup time was (sec) 1.240000 now iterating at: 12:42:16 rms-change max change #iterations 10.42958 413.6019 at 10iterations 6.117127 136.7804 at 20iterations 3.600233 68.56813 at 30iterations 2.108325 43.18071 at 40iterations 1.231049 22.71374 at 50iterations 0.7192910 12.69695 at 60iterations 0.4192287 7.756526 at 70iterations 0.2446918 4.317190 at 80iterations 0.1423428 2.376543 at 90iterations 8.3007425E-02 1.420891 at 100iterations 4.8473671E-02 0.9755669 at 110iterations 2.8376415E-02 0.4840240 at 120iterations 1.6758036E-02 0.3008833 at 130iterations 1.0034917E-02 0.1919174 at 140iterations 6.1684381E-03 0.1341476 at 150iterations 3.9535780E-03 8.6551666E-02 at 160iterations 2.6812106E-03 5.7519913E-02 at 170iterations 1.9334360E-03 4.7531128E-02 at 180iterations finished qdiffx linear iterations at : 12:42:27 total time elapsed so far: 12.45000 # loops : 180 mean,max change (kT/e) : 1.9334360E-03 4.7531128E-02 energy calculations done at 12.45000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.58000 DelPhi exited at 12:42:28 12.587u 0.207s 0:13.09 97.6% 0+0k 0+0io 0pf+0w