Sun Oct 9 14:05:17 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 14:05:17 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 = 2364 !!! WARNING: GLM 182 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: 0.6849315 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): 22.51100 71.48100 ymin,ymax (A): -2.114000 49.86200 zmin,zma (A): -6.262000 36.81800 x,y,z range (A): 48.96999 51.97600 43.08000 scale (grids/A): 0.6849315 object centre (A): 46.99600 23.87400 15.27800 number of atom coordinates read : 2364 total number of charged atoms : 2218 net assigned charge : 3.406023 assigned positive charge : 363.1382 centred at (gu) : 90.32124 89.37640 89.34916 assigned negative charge : -359.7326 centred at (gu) : 90.35213 89.24589 89.25603 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7567 nv = 96 ne = 84 npr = 47314 no. pairs analyzed = 47314 no. exposed pairs = 2905 no. arc points = 20492 no. surface atoms = 979 nbur = 1385 mkacc time = 8.0000006E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 443 mr = 4212 m= 5 mr = 73 m= 0 mr = 0 time to grow re-entrant surface = 8.9999996E-02 no. cavity mid-points inaccessible to solvent = 9 time to turn everything in is 0.1900000 number of dielectric boundary points 3730 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1968 ## 208 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 8591 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.6936369E-08 4.2561929E-08 midg,1,midg; midg,igrid,midg -3.1593284E-08 5.3702319E-08 1,midg,midg; igrid,midg,midg 2.5949966E-08 7.0967143E-09 gauss-seidel spectral radius is 0.9889266 estimated iterations to convergence 77 setup time was (sec) 0.3800000 now iterating at: 14:05:17 rms-change max change #iterations 0.1878105 25.86882 at 10iterations 2.1957600E-02 2.903118 at 20iterations 2.9446597E-03 0.3615036 at 30iterations 5.3745502E-04 7.7056885E-02 at 40iterations 1.4504473E-04 2.1093369E-02 at 50iterations finished qdiffx linear iterations at : 14:05:20 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 1.4504473E-04 2.1093369E-02 energy calculations done at 3.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 14:05:21 3.395u 0.172s 0:03.90 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 14:05:21 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 = 2364 !!! WARNING: GLM 182 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.054795 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): 22.51100 71.48100 ymin,ymax (A): -2.114000 49.86200 zmin,zma (A): -6.262000 36.81800 x,y,z range (A): 48.96999 51.97600 43.08000 scale (grids/A): 2.054795 object centre (A): 46.99600 23.87400 15.27800 number of atom coordinates read : 2364 total number of charged atoms : 2218 net assigned charge : 3.406023 assigned positive charge : 363.1382 centred at (gu) : 90.96310 88.12878 88.04705 assigned negative charge : -359.7326 centred at (gu) : 91.05619 87.73730 87.76789 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 80401 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20492 grid for indexing accessible points = 1.400000 m= 30778 mr = 56169 m= 5294 mr = 23084 m= 415 mr = 3274 m= 11 mr = 199 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 1707 time to turn everything in is 0.4100000 number of dielectric boundary points 34173 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 114 iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 17569 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) : 0.6849315 object centre at (A) : 46.99600 23.87400 15.27800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.5418724E-03 4.9189609E-02 midg,1,midg; midg,igrid,midg -3.1888857E-02 2.0112008E-02 1,midg,midg; igrid,midg,midg 3.6107019E-02 -1.3749266E-02 gauss-seidel spectral radius is 0.9987990 estimated iterations to convergence 228 setup time was (sec) 0.6200000 now iterating at: 14:05:21 rms-change max change #iterations 4.749225 217.6470 at 10iterations 2.322203 81.59160 at 20iterations 1.141983 37.41235 at 30iterations 0.5627586 16.91434 at 40iterations 0.2770394 8.176319 at 50iterations 0.1356015 3.983468 at 60iterations 6.6915378E-02 2.025208 at 70iterations 3.2908473E-02 0.9507647 at 80iterations 1.6295969E-02 0.4608440 at 90iterations 8.0927107E-03 0.2367325 at 100iterations 4.0454292E-03 0.1129036 at 110iterations 2.0712602E-03 6.2023163E-02 at 120iterations finished qdiffx linear iterations at : 14:05:29 total time elapsed so far: 7.750000 # loops : 120 mean,max change (kT/e) : 2.0712602E-03 6.2023163E-02 energy calculations done at 7.760000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.890000 DelPhi exited at 14:05:29 7.889u 0.202s 0:08.37 96.5% 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 Sun Oct 9 2011 at 14:05:29 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 = 2364 !!! WARNING: GLM 182 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: 3.082192 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): 22.51100 71.48100 ymin,ymax (A): -2.114000 49.86200 zmin,zma (A): -6.262000 36.81800 x,y,z range (A): 48.96999 51.97600 43.08000 scale (grids/A): 3.082192 object centre (A): 46.99600 23.87400 15.27800 number of atom coordinates read : 2364 total number of charged atoms : 2218 net assigned charge : 3.406023 assigned positive charge : 363.1382 centred at (gu) : 91.44451 87.19302 87.07040 assigned negative charge : -359.7326 centred at (gu) : 91.58424 86.60599 86.65189 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 185562 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20492 grid for indexing accessible points = 1.400000 m= 97834 mr = 135906 m= 37636 mr = 80573 m= 9790 mr = 30673 m= 1682 mr = 7281 m= 172 mr = 1155 m= 3 mr = 108 m= 0 mr = 0 time to grow re-entrant surface = 0.6100000 no. cavity mid-points inaccessible to solvent = 5561 time to turn everything in is 1.190000 number of dielectric boundary points 76983 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.280000 number of grid points assigned charge 17734 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) : 2.054795 object centre at (A) : 46.99600 23.87400 15.27800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.2205777E-02 0.4368348 midg,1,midg; midg,igrid,midg -0.3802894 0.4548832 1,midg,midg; igrid,midg,midg 0.4364130 -0.3974033 gauss-seidel spectral radius is 0.9992917 estimated iterations to convergence 296 setup time was (sec) 1.430000 now iterating at: 14:05:31 rms-change max change #iterations 10.77094 424.7886 at 10iterations 6.340721 171.2430 at 20iterations 3.733854 81.56316 at 30iterations 2.195549 39.94983 at 40iterations 1.288556 22.38945 at 50iterations 0.7559229 13.71916 at 60iterations 0.4419467 7.950215 at 70iterations 0.2584273 4.231201 at 80iterations 0.1507292 2.752948 at 90iterations 8.8040918E-02 1.609674 at 100iterations 5.1395260E-02 0.8875141 at 110iterations 3.0043744E-02 0.6291962 at 120iterations 1.7601188E-02 0.3125877 at 130iterations 1.0346662E-02 0.1677704 at 140iterations 6.1290287E-03 0.1059456 at 150iterations 3.6659287E-03 7.2284698E-02 at 160iterations 2.2510798E-03 4.1206360E-02 at 170iterations 1.4311615E-03 2.7873993E-02 at 180iterations finished qdiffx linear iterations at : 14:05:42 total time elapsed so far: 12.87000 # loops : 180 mean,max change (kT/e) : 1.4311615E-03 2.7873993E-02 energy calculations done at 12.87000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.01000 DelPhi exited at 14:05:43 13.008u 0.216s 0:13.59 97.2% 0+0k 0+0io 0pf+0w