Sat Oct 15 13:46:27 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 15 2011 at 13:46:27 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2296 !!! WARNING: GLM 55 has a net charge of -0.0940 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: 0.6145454 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): -6.148000 39.61600 ymin,ymax (A): 14.02500 71.95400 zmin,zma (A): -0.7990000 48.52400 x,y,z range (A): 45.76400 57.92900 49.32300 scale (grids/A): 0.6145454 object centre (A): 16.73400 42.98950 23.86250 number of atom coordinates read : 2296 total number of charged atoms : 2213 net assigned charge : -2.094001 assigned positive charge : 339.1563 centred at (gu) : 90.41863 90.19016 88.21548 assigned negative charge : -341.2509 centred at (gu) : 90.45441 90.27337 88.15042 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.0000000E-02 boundary points on vw surface= 5842 nv = 96 ne = 84 npr = 46073 no. pairs analyzed = 46073 no. exposed pairs = 3056 no. arc points = 21226 no. surface atoms = 1033 nbur = 1263 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 302 mr = 3045 m= 0 mr = 22 time to grow re-entrant surface = 8.0000013E-02 no. cavity mid-points inaccessible to solvent = 1 time to turn everything in is 0.1700000 number of dielectric boundary points 3077 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2168 ## 227 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 7258 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.8581456E-09 1.2346346E-09 midg,1,midg; midg,igrid,midg 2.6371332E-09 -5.7430922E-09 1,midg,midg; igrid,midg,midg 3.8776551E-10 -3.4207019E-09 gauss-seidel spectral radius is 0.9862689 estimated iterations to convergence 70 setup time was (sec) 0.3600000 now iterating at: 13:46:28 rms-change max change #iterations 0.1115990 17.67068 at 10iterations 1.0136863E-02 1.576130 at 20iterations 9.3904836E-04 0.1377354 at 30iterations 1.1131263E-04 1.5119553E-02 at 40iterations 2.1238518E-05 2.9850006E-03 at 50iterations finished qdiffx linear iterations at : 13:46:32 total time elapsed so far: 3.380000 # loops : 50 mean,max change (kT/e) : 2.1238518E-05 2.9850006E-03 energy calculations done at 3.380000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.510000 DelPhi exited at 13:46:33 3.516u 0.206s 0:05.51 67.3% 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 Sat Oct 15 2011 at 13:46:33 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2296 !!! WARNING: GLM 55 has a net charge of -0.0940 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: 1.843636 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): -6.148000 39.61600 ymin,ymax (A): 14.02500 71.95400 zmin,zma (A): -0.7990000 48.52400 x,y,z range (A): 45.76400 57.92900 49.32300 scale (grids/A): 1.843636 object centre (A): 16.73400 42.98950 23.86250 number of atom coordinates read : 2296 total number of charged atoms : 2213 net assigned charge : -2.094001 assigned positive charge : 339.1563 centred at (gu) : 91.25559 90.57010 84.64597 assigned negative charge : -341.2509 centred at (gu) : 91.36311 90.82008 84.45120 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 63872 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21226 grid for indexing accessible points = 1.400000 m= 21757 mr = 43436 m= 3095 mr = 15227 m= 190 mr = 1774 m= 3 mr = 49 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 857 time to turn everything in is 0.3200000 number of dielectric boundary points 28431 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 135 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 17324 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) : 0.6145454 object centre at (A) : 16.73400 42.98950 23.86250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.9349852E-02 9.7331256E-03 midg,1,midg; midg,igrid,midg 3.9627321E-02 -3.7391852E-03 1,midg,midg; igrid,midg,midg -3.7759347E-03 -1.9933164E-02 gauss-seidel spectral radius is 0.9985223 estimated iterations to convergence 206 setup time was (sec) 0.5700000 now iterating at: 13:46:34 rms-change max change #iterations 3.696600 186.4702 at 10iterations 1.676122 64.05020 at 20iterations 0.7627966 26.56387 at 30iterations 0.3462541 12.94302 at 40iterations 0.1577068 5.907238 at 50iterations 7.1758457E-02 2.439691 at 60iterations 3.2483749E-02 1.108184 at 70iterations 1.4796171E-02 0.5292244 at 80iterations 6.7689698E-03 0.2362065 at 90iterations 3.0701645E-03 0.1028004 at 100iterations 1.4033077E-03 5.1632285E-02 at 110iterations 6.4161245E-04 2.2071123E-02 at 120iterations finished qdiffx linear iterations at : 13:46:46 total time elapsed so far: 8.480000 # loops : 120 mean,max change (kT/e) : 6.4161245E-04 2.2071123E-02 energy calculations done at 8.480000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.610000 DelPhi exited at 13:46:47 8.614u 0.314s 0:14.27 62.5% 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 15 2011 at 13:46:47 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2296 !!! WARNING: GLM 55 has a net charge of -0.0940 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: 2.765454 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): -6.148000 39.61600 ymin,ymax (A): 14.02500 71.95400 zmin,zma (A): -0.7990000 48.52400 x,y,z range (A): 45.76400 57.92900 49.32300 scale (grids/A): 2.765454 object centre (A): 16.73400 42.98950 23.86250 number of atom coordinates read : 2296 total number of charged atoms : 2213 net assigned charge : -2.094001 assigned positive charge : 339.1563 centred at (gu) : 91.88326 90.85497 81.96872 assigned negative charge : -341.2509 centred at (gu) : 92.04463 91.23008 81.67686 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 147778 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21226 grid for indexing accessible points = 1.400000 m= 71262 mr = 105626 m= 24347 mr = 56661 m= 5419 mr = 18812 m= 738 mr = 3899 m= 37 mr = 430 m= 2 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.4900000 no. cavity mid-points inaccessible to solvent = 2893 time to turn everything in is 0.8600000 number of dielectric boundary points 64142 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 0.9600000 number of grid points assigned charge 17702 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) : 1.843636 object centre at (A) : 16.73400 42.98950 23.86250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3872691 0.1601841 midg,1,midg; midg,igrid,midg 0.4439374 -1.4119299E-02 1,midg,midg; igrid,midg,midg -4.6056669E-02 -0.2044702 gauss-seidel spectral radius is 0.9992272 estimated iterations to convergence 284 setup time was (sec) 1.130000 now iterating at: 13:46:49 rms-change max change #iterations 8.898766 390.9835 at 10iterations 5.173007 114.4503 at 20iterations 2.982970 62.29185 at 30iterations 1.711553 36.19221 at 40iterations 0.9805983 21.12217 at 50iterations 0.5628108 11.36192 at 60iterations 0.3210447 6.484711 at 70iterations 0.1827627 3.611969 at 80iterations 0.1046479 2.189411 at 90iterations 5.9349876E-02 1.128071 at 100iterations 3.3859681E-02 0.6263342 at 110iterations 1.9256897E-02 0.4304562 at 120iterations 1.0935202E-02 0.2018948 at 130iterations 6.2313504E-03 0.1280947 at 140iterations 3.5474736E-03 7.4020386E-02 at 150iterations 2.0264285E-03 3.8938761E-02 at 160iterations 1.1630926E-03 2.2068024E-02 at 170iterations 6.6984177E-04 1.4385223E-02 at 180iterations finished qdiffx linear iterations at : 13:47:11 total time elapsed so far: 13.87000 # loops : 180 mean,max change (kT/e) : 6.6984177E-04 1.4385223E-02 energy calculations done at 13.87000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.01000 DelPhi exited at 13:47:12 14.008u 0.293s 0:24.61 58.0% 0+0k 0+0io 0pf+0w