Sun Oct 9 16:44:03 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 Sun Oct 9 2011 at 16:44:03 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2359 !!! WARNING: ASL 42 has a net charge of -0.1000 !!! WARNING: GLM 48 has a net charge of -0.0940 !!! WARNING: GLM 120 has a net charge of -0.0940 !!! WARNING: LYS 255 has a net charge of -0.0450 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: 0.6655948 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): -52.75800 -3.259000 ymin,ymax (A): 5.427000 52.57500 zmin,zma (A): -25.03200 28.45400 x,y,z range (A): 49.49900 47.14799 53.48600 scale (grids/A): 0.6655948 object centre (A): -28.00850 29.00100 1.711000 number of atom coordinates read : 2359 total number of charged atoms : 2273 net assigned charge : -0.3329902 assigned positive charge : 352.7601 centred at (gu) : 88.89082 88.96083 88.56059 assigned negative charge : -353.0939 centred at (gu) : 88.93082 89.04152 88.65068 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 7272 nv = 96 ne = 84 npr = 46873 no. pairs analyzed = 46873 no. exposed pairs = 3032 no. arc points = 21594 no. surface atoms = 1031 nbur = 1328 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 419 mr = 3968 m= 0 mr = 46 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1700000 number of dielectric boundary points 3677 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2028 ## 172 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 8459 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.2953000E-08 -1.5083151E-08 midg,1,midg; midg,igrid,midg 1.8682414E-08 -1.4795256E-08 1,midg,midg; igrid,midg,midg 8.4567731E-09 -7.8290379E-09 gauss-seidel spectral radius is 0.9882839 estimated iterations to convergence 75 setup time was (sec) 0.3600000 now iterating at: 16:44:03 rms-change max change #iterations 0.1642539 22.97471 at 10iterations 1.7586851E-02 2.499763 at 20iterations 1.9379617E-03 0.2886200 at 30iterations 2.4273928E-04 3.1616211E-02 at 40iterations 5.0406215E-05 7.1907043E-03 at 50iterations finished qdiffx linear iterations at : 16:44:06 total time elapsed so far: 3.190000 # loops : 50 mean,max change (kT/e) : 5.0406215E-05 7.1907043E-03 energy calculations done at 3.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.330000 DelPhi exited at 16:44:07 3.330u 0.169s 0:03.76 92.8% 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 16:44:07 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2359 !!! WARNING: ASL 42 has a net charge of -0.1000 !!! WARNING: GLM 48 has a net charge of -0.0940 !!! WARNING: GLM 120 has a net charge of -0.0940 !!! WARNING: LYS 255 has a net charge of -0.0450 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: 1.996784 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): -52.75800 -3.259000 ymin,ymax (A): 5.427000 52.57500 zmin,zma (A): -25.03200 28.45400 x,y,z range (A): 49.49900 47.14799 53.48600 scale (grids/A): 1.996784 object centre (A): -28.00850 29.00100 1.711000 number of atom coordinates read : 2359 total number of charged atoms : 2273 net assigned charge : -0.3329902 assigned positive charge : 352.7601 centred at (gu) : 86.67175 86.88200 85.68135 assigned negative charge : -353.0939 centred at (gu) : 86.79227 87.12445 85.95210 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 77346 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21594 grid for indexing accessible points = 1.400000 m= 28798 mr = 53243 m= 5085 mr = 21045 m= 334 mr = 3216 m= 5 mr = 107 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 0.3800000 number of dielectric boundary points 33957 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 127 iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 17933 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) : 0.6655948 object centre at (A) : -28.00850 29.00100 1.711000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.3516187E-03 9.4931340E-03 midg,1,midg; midg,igrid,midg -8.6698690E-03 -1.1792125E-02 1,midg,midg; igrid,midg,midg 3.8568221E-03 -1.2018727E-02 gauss-seidel spectral radius is 0.9987391 estimated iterations to convergence 223 setup time was (sec) 0.5900000 now iterating at: 16:44:07 rms-change max change #iterations 4.460639 174.1976 at 10iterations 2.152027 79.43266 at 20iterations 1.039376 37.00443 at 30iterations 0.5020710 18.31587 at 40iterations 0.2425282 7.295448 at 50iterations 0.1167475 3.817902 at 60iterations 5.6575451E-02 1.676439 at 70iterations 2.7387129E-02 0.8276367 at 80iterations 1.3216563E-02 0.4429932 at 90iterations 6.3997321E-03 0.1957459 at 100iterations 3.0984608E-03 9.2350006E-02 at 110iterations 1.5020886E-03 4.4829369E-02 at 120iterations finished qdiffx linear iterations at : 16:44:14 total time elapsed so far: 7.610000 # loops : 120 mean,max change (kT/e) : 1.5020886E-03 4.4829369E-02 energy calculations done at 7.610000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.740000 DelPhi exited at 16:44:15 7.746u 0.194s 0:08.19 96.8% 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 16:44:15 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2359 !!! WARNING: ASL 42 has a net charge of -0.1000 !!! WARNING: GLM 48 has a net charge of -0.0940 !!! WARNING: GLM 120 has a net charge of -0.0940 !!! WARNING: LYS 255 has a net charge of -0.0450 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: 2.995176 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): -52.75800 -3.259000 ymin,ymax (A): 5.427000 52.57500 zmin,zma (A): -25.03200 28.45400 x,y,z range (A): 49.49900 47.14799 53.48600 scale (grids/A): 2.995176 object centre (A): -28.00850 29.00100 1.711000 number of atom coordinates read : 2359 total number of charged atoms : 2273 net assigned charge : -0.3329902 assigned positive charge : 352.7601 centred at (gu) : 85.00764 85.32289 83.52188 assigned negative charge : -353.0939 centred at (gu) : 85.18848 85.68658 83.92811 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 178601 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21594 grid for indexing accessible points = 1.400000 m= 90695 mr = 128946 m= 35124 mr = 73492 m= 9478 mr = 28359 m= 1497 mr = 7143 m= 109 mr = 972 m= 1 mr = 35 m= 0 mr = 0 time to grow re-entrant surface = 0.5700001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.000000 number of dielectric boundary points 76558 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 18184 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) : 1.996784 object centre at (A) : -28.00850 29.00100 1.711000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.2032803E-02 0.3100326 midg,1,midg; midg,igrid,midg -0.1792020 -0.2195525 1,midg,midg; igrid,midg,midg -2.5621569E-02 -0.1546777 gauss-seidel spectral radius is 0.9992918 estimated iterations to convergence 296 setup time was (sec) 1.220000 now iterating at: 16:44:16 rms-change max change #iterations 10.31525 476.4152 at 10iterations 6.113155 134.5107 at 20iterations 3.624540 68.02445 at 30iterations 2.142649 48.52367 at 40iterations 1.259610 26.59320 at 50iterations 0.7388041 14.34776 at 60iterations 0.4338695 8.909349 at 70iterations 0.2543529 4.772301 at 80iterations 0.1486422 2.887446 at 90iterations 8.6878836E-02 1.599072 at 100iterations 5.0758086E-02 0.9903071 at 110iterations 2.9668750E-02 0.5089248 at 120iterations 1.7289095E-02 0.3047552 at 130iterations 1.0096098E-02 0.1733646 at 140iterations 5.8855633E-03 0.1065402 at 150iterations 3.4411103E-03 5.8798790E-02 at 160iterations 2.0126870E-03 3.8284302E-02 at 170iterations 1.1822521E-03 2.1270752E-02 at 180iterations finished qdiffx linear iterations at : 16:44:28 total time elapsed so far: 12.61000 # loops : 180 mean,max change (kT/e) : 1.1822521E-03 2.1270752E-02 energy calculations done at 12.61000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.74000 DelPhi exited at 16:44:28 12.744u 0.227s 0:13.24 97.8% 0+0k 0+0io 0pf+0w