Sun Oct 9 16:10:05 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 16:10:05 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3163 !!! WARNING: GLM 171 has a net charge of -0.0940 !!! WARNING: GLM 240 has a net charge of -0.0940 !!! WARNING: MG4 470 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5974057 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): -15.18500 37.71400 ymin,ymax (A): -56.13900 -3.979000 zmin,zma (A): -7.227000 52.36400 x,y,z range (A): 52.89900 52.16000 59.59100 scale (grids/A): 0.5974057 object centre (A): 11.26450 -30.05900 22.56850 number of atom coordinates read : 3163 total number of charged atoms : 3011 net assigned charge : -5.287977 assigned positive charge : 469.4349 centred at (gu) : 89.93362 89.07024 91.83470 assigned negative charge : -474.7243 centred at (gu) : 89.94862 88.98191 91.86600 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7313 nv = 96 ne = 84 npr = 65711 no. pairs analyzed = 65711 no. exposed pairs = 3812 no. arc points = 26570 no. surface atoms = 1280 nbur = 1883 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 381 mr = 4022 m= 1 mr = 43 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 11 time to turn everything in is 0.2300000 number of dielectric boundary points 3630 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2653 ## 270 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 9318 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.0737659E-10 -4.9971902E-09 midg,1,midg; midg,igrid,midg -7.0073840E-09 1.2531176E-09 1,midg,midg; igrid,midg,midg -1.4131598E-09 -2.5830849E-09 gauss-seidel spectral radius is 0.9855437 estimated iterations to convergence 68 setup time was (sec) 0.4200000 now iterating at: 16:10:06 rms-change max change #iterations 0.1208948 17.97656 at 10iterations 1.0094896E-02 1.458174 at 20iterations 8.4459968E-04 0.1204987 at 30iterations 7.4199306E-05 1.0381699E-02 at 40iterations 8.5319925E-06 1.4574528E-03 at 50iterations finished qdiffx linear iterations at : 16:10:08 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 8.5319925E-06 1.4574528E-03 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 16:10:09 3.396u 0.165s 0:03.86 91.9% 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 16:10:09 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3163 !!! WARNING: GLM 171 has a net charge of -0.0940 !!! WARNING: GLM 240 has a net charge of -0.0940 !!! WARNING: MG4 470 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.792217 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): -15.18500 37.71400 ymin,ymax (A): -56.13900 -3.979000 zmin,zma (A): -7.227000 52.36400 x,y,z range (A): 52.89900 52.16000 59.59100 scale (grids/A): 1.792217 object centre (A): 11.26450 -30.05900 22.56850 number of atom coordinates read : 3163 total number of charged atoms : 3011 net assigned charge : -5.287977 assigned positive charge : 469.4349 centred at (gu) : 89.80016 87.20950 95.50335 assigned negative charge : -474.7243 centred at (gu) : 89.84553 86.94541 95.59779 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 80806 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26570 grid for indexing accessible points = 1.400000 m= 27480 mr = 56535 m= 4136 mr = 19816 m= 195 mr = 2512 m= 3 mr = 63 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 1160 time to turn everything in is 0.3800000 number of dielectric boundary points 33694 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 217 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 23461 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) : 0.5974057 object centre at (A) : 11.26450 -30.05900 22.56850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.8031205E-03 7.6113297E-03 midg,1,midg; midg,igrid,midg -1.7485505E-02 -1.2556127E-02 1,midg,midg; igrid,midg,midg -3.0942027E-02 -2.1048173E-02 gauss-seidel spectral radius is 0.9985088 estimated iterations to convergence 205 setup time was (sec) 0.6000000 now iterating at: 16:10:10 rms-change max change #iterations 4.218040 178.0099 at 10iterations 1.904711 72.61665 at 20iterations 0.8595798 29.37259 at 30iterations 0.3898740 12.12485 at 40iterations 0.1758055 5.233696 at 50iterations 7.9845749E-02 2.765535 at 60iterations 3.6035873E-02 1.161764 at 70iterations 1.6354298E-02 0.4980240 at 80iterations 7.4128215E-03 0.2203093 at 90iterations 3.3597592E-03 9.9967957E-02 at 100iterations 1.5225067E-03 4.6452284E-02 at 110iterations 6.8963191E-04 2.1461487E-02 at 120iterations finished qdiffx linear iterations at : 16:10:17 total time elapsed so far: 7.630000 # loops : 120 mean,max change (kT/e) : 6.8963191E-04 2.1461487E-02 energy calculations done at 7.630000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.770000 DelPhi exited at 16:10:17 7.777u 0.199s 0:08.27 96.2% 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 16:10:17 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3163 !!! WARNING: GLM 171 has a net charge of -0.0940 !!! WARNING: GLM 240 has a net charge of -0.0940 !!! WARNING: MG4 470 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.688325 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): -15.18500 37.71400 ymin,ymax (A): -56.13900 -3.979000 zmin,zma (A): -7.227000 52.36400 x,y,z range (A): 52.89900 52.16000 59.59100 scale (grids/A): 2.688325 object centre (A): 11.26450 -30.05900 22.56850 number of atom coordinates read : 3163 total number of charged atoms : 3011 net assigned charge : -5.287977 assigned positive charge : 469.4349 centred at (gu) : 89.69999 85.81408 98.25483 assigned negative charge : -474.7243 centred at (gu) : 89.76810 85.41810 98.39665 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 187616 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26570 grid for indexing accessible points = 1.400000 m= 91060 mr = 137953 m= 31218 mr = 73529 m= 7099 mr = 24501 m= 861 mr = 5310 m= 36 mr = 548 m= 0 mr = 13 time to grow re-entrant surface = 0.5700001 no. cavity mid-points inaccessible to solvent = 3516 time to turn everything in is 1.000000 number of dielectric boundary points 76036 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.100000 number of grid points assigned charge 24085 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) : 1.792217 object centre at (A) : 11.26450 -30.05900 22.56850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1627802 0.1102129 midg,1,midg; midg,igrid,midg -0.1684023 -0.1947620 1,midg,midg; igrid,midg,midg -0.4933663 -0.2658803 gauss-seidel spectral radius is 0.9992354 estimated iterations to convergence 285 setup time was (sec) 1.240000 now iterating at: 16:10:19 rms-change max change #iterations 10.20039 301.2607 at 10iterations 5.915103 138.4629 at 20iterations 3.408563 74.76765 at 30iterations 1.954307 43.82504 at 40iterations 1.124488 25.27104 at 50iterations 0.6429231 13.66154 at 60iterations 0.3686011 7.124908 at 70iterations 0.2104212 3.911743 at 80iterations 0.1200649 2.180830 at 90iterations 6.8436548E-02 1.258232 at 100iterations 3.9050784E-02 0.6904316 at 110iterations 2.2245642E-02 0.4081917 at 120iterations 1.2694254E-02 0.2183418 at 130iterations 7.2284332E-03 0.1299853 at 140iterations 4.1188891E-03 7.3677063E-02 at 150iterations 2.3442688E-03 4.0226460E-02 at 160iterations 1.3380861E-03 2.4669647E-02 at 170iterations 7.6328474E-04 1.4204025E-02 at 180iterations finished qdiffx linear iterations at : 16:10:30 total time elapsed so far: 12.64000 # loops : 180 mean,max change (kT/e) : 7.6328474E-04 1.4204025E-02 energy calculations done at 12.64000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.77000 DelPhi exited at 16:10:30 12.776u 0.205s 0:13.24 97.9% 0+0k 0+0io 0pf+0w