Mon Oct 10 17:04:59 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 17:04:59 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: 324 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3734 !!! WARNING: GLM 478 has a net charge of -0.0940 !!! WARNING: HEM 900 has a net charge of 1.4000 !!! WARNING: ZN9 951 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5528809 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): -30.08500 30.91600 ymin,ymax (A): -29.37500 35.01500 zmin,zma (A): 30.75700 86.52100 x,y,z range (A): 61.00100 64.39000 55.76400 scale (grids/A): 0.5528809 object centre (A): 0.4155006 2.820000 58.63900 number of atom coordinates read : 3734 total number of charged atoms : 3535 net assigned charge : 5.206025 assigned positive charge : 561.9238 centred at (gu) : 90.79413 90.81623 90.97706 assigned negative charge : -556.7195 centred at (gu) : 90.92090 90.85843 90.95325 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 7306 nv = 96 ne = 84 npr = 75485 no. pairs analyzed = 75485 no. exposed pairs = 4881 no. arc points = 33856 no. surface atoms = 1626 nbur = 2108 mkacc time = 0.1800000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 303 mr = 3742 m= 0 mr = 10 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4500000 number of dielectric boundary points 3857 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3406 ## 408 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 9605 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4596217E-10 8.7646196E-10 midg,1,midg; midg,igrid,midg 7.2748324E-10 -2.6590570E-11 1,midg,midg; igrid,midg,midg 1.4601559E-09 -1.1551577E-09 gauss-seidel spectral radius is 0.9831875 estimated iterations to convergence 63 setup time was (sec) 0.7100000 now iterating at: 17:05:00 rms-change max change #iterations 9.0539768E-02 16.11329 at 10iterations 6.6800741E-03 0.9251900 at 20iterations 1.0365355E-03 0.1745453 at 30iterations 3.2701591E-04 5.6171417E-02 at 40iterations 1.1438282E-04 1.9660950E-02 at 50iterations finished qdiffx linear iterations at : 17:05:03 total time elapsed so far: 3.580000 # loops : 50 mean,max change (kT/e) : 1.1438282E-04 1.9660950E-02 energy calculations done at 3.580000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.770000 DelPhi exited at 17:05:04 3.776u 0.211s 0:04.59 86.7% 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 17:05:04 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: 324 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3734 !!! WARNING: GLM 478 has a net charge of -0.0940 !!! WARNING: HEM 900 has a net charge of 1.4000 !!! WARNING: ZN9 951 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.658643 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): -30.08500 30.91600 ymin,ymax (A): -29.37500 35.01500 zmin,zma (A): 30.75700 86.52100 x,y,z range (A): 61.00100 64.39000 55.76400 scale (grids/A): 1.658643 object centre (A): 0.4155006 2.820000 58.63900 number of atom coordinates read : 3734 total number of charged atoms : 3535 net assigned charge : 5.206025 assigned positive charge : 561.9238 centred at (gu) : 92.38125 92.44720 92.93040 assigned negative charge : -556.7195 centred at (gu) : 92.76247 92.57474 92.85918 start vw surface at 0.2100000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 80812 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33856 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 24594 mr = 54243 m= 2653 mr = 16532 m= 94 mr = 1350 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6500000 number of dielectric boundary points 36025 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 379 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 27184 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) : 0.5528809 object centre at (A) : 0.4155006 2.820000 58.63900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.0056516E-03 1.8926864E-03 midg,1,midg; midg,igrid,midg 2.1175927E-02 -1.1735266E-02 1,midg,midg; igrid,midg,midg 1.9813240E-02 3.4506204E-05 gauss-seidel spectral radius is 0.9983209 estimated iterations to convergence 194 setup time was (sec) 0.9700000 now iterating at: 17:05:05 rms-change max change #iterations 3.907521 163.3502 at 10iterations 1.686875 62.23447 at 20iterations 0.7277246 24.84608 at 30iterations 0.3132668 10.18907 at 40iterations 0.1350535 4.421906 at 50iterations 5.8363009E-02 1.865785 at 60iterations 2.5216762E-02 0.8597565 at 70iterations 1.0943535E-02 0.3613889 at 80iterations 4.8267785E-03 0.1585789 at 90iterations 2.1932113E-03 6.6400051E-02 at 100iterations 1.0532531E-03 3.8646698E-02 at 110iterations 5.5356306E-04 1.9048691E-02 at 120iterations finished qdiffx linear iterations at : 17:05:12 total time elapsed so far: 8.070000 # loops : 120 mean,max change (kT/e) : 5.5356306E-04 1.9048691E-02 energy calculations done at 8.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.260000 DelPhi exited at 17:05:13 8.263u 0.260s 0:09.21 92.5% 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 Mon Oct 10 2011 at 17:05:13 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: 324 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3734 !!! WARNING: GLM 478 has a net charge of -0.0940 !!! WARNING: HEM 900 has a net charge of 1.4000 !!! WARNING: ZN9 951 has a net charge of 1.4000 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: 2.487964 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): -30.08500 30.91600 ymin,ymax (A): -29.37500 35.01500 zmin,zma (A): 30.75700 86.52100 x,y,z range (A): 61.00100 64.39000 55.76400 scale (grids/A): 2.487964 object centre (A): 0.4155006 2.820000 58.63900 number of atom coordinates read : 3734 total number of charged atoms : 3535 net assigned charge : 5.206025 assigned positive charge : 561.9238 centred at (gu) : 93.57169 93.67066 94.39527 assigned negative charge : -556.7195 centred at (gu) : 94.14363 93.86206 94.28868 start vw surface at 0.1900000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 187944 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33856 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 85428 mr = 133259 m= 24146 mr = 66789 m= 4259 mr = 17831 m= 384 mr = 2882 m= 9 mr = 186 m= 0 mr = 2 time to grow re-entrant surface = 0.8700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.520000 number of dielectric boundary points 81221 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 21 iepsmp to db, and charging done at 1.680000 number of grid points assigned charge 28253 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) : 1.658643 object centre at (A) : 0.4155006 2.820000 58.63900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.1029179E-02 3.6280196E-02 midg,1,midg; midg,igrid,midg 0.8428249 -0.1246726 1,midg,midg; igrid,midg,midg 0.2802572 2.6292279E-02 gauss-seidel spectral radius is 0.9991965 estimated iterations to convergence 279 setup time was (sec) 1.860000 now iterating at: 17:05:15 rms-change max change #iterations 10.03415 263.6211 at 10iterations 5.763741 132.8676 at 20iterations 3.300792 74.42098 at 30iterations 1.879112 41.49216 at 40iterations 1.065553 21.40575 at 50iterations 0.6039487 12.20504 at 60iterations 0.3415262 8.783894 at 70iterations 0.1928289 4.057640 at 80iterations 0.1087089 2.440458 at 90iterations 6.1289601E-02 1.219719 at 100iterations 3.4552567E-02 0.6818047 at 110iterations 1.9443562E-02 0.4176521 at 120iterations 1.0967830E-02 0.2314529 at 130iterations 6.1998097E-03 0.1283131 at 140iterations 3.5020155E-03 7.2940826E-02 at 150iterations 1.9897532E-03 3.9096914E-02 at 160iterations 1.1449486E-03 2.2178650E-02 at 170iterations 6.7211484E-04 1.3668060E-02 at 180iterations finished qdiffx linear iterations at : 17:05:27 total time elapsed so far: 13.54000 # loops : 180 mean,max change (kT/e) : 6.7211484E-04 1.3668060E-02 energy calculations done at 13.54000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.73000 DelPhi exited at 17:05:28 13.734u 0.287s 0:14.92 93.9% 0+0k 0+0io 0pf+0w