Mon Oct 10 19:37:10 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+sph.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 = amb.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 19:37:11 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2665 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5616825 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): -9.447001 40.28000 ymin,ymax (A): -9.684999 40.89100 zmin,zma (A): -0.8190000 62.56200 x,y,z range (A): 49.72700 50.57600 63.38100 scale (grids/A): 0.5616825 object centre (A): 15.41650 15.60300 30.87150 number of atom coordinates read : 2665 total number of charged atoms : 2528 net assigned charge : 4.500024 assigned positive charge : 390.9908 centred at (gu) : 90.43048 89.45020 89.31905 assigned negative charge : -386.4918 centred at (gu) : 90.32439 89.31951 89.33575 start vw surface at 0.1200000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 5763 nv = 96 ne = 84 npr = 50982 no. pairs analyzed = 50982 no. exposed pairs = 3756 no. arc points = 26354 no. surface atoms = 1245 nbur = 1420 mkacc time = 0.1300000 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 = 1.540000 m= 268 mr = 2878 m= 0 mr = 16 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 3137 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2577 ## 286 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 7223 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.0280044E-10 2.9251618E-10 midg,1,midg; midg,igrid,midg -9.7158492E-10 1.6001824E-09 1,midg,midg; igrid,midg,midg -5.2513321E-10 1.7568281E-09 gauss-seidel spectral radius is 0.9836361 estimated iterations to convergence 64 setup time was (sec) 0.5800000 now iterating at: 19:37:11 rms-change max change #iterations 7.7557065E-02 14.84310 at 10iterations 5.6399787E-03 1.034424 at 20iterations 4.3231508E-04 7.4348450E-02 at 30iterations 4.0053776E-05 6.1092377E-03 at 40iterations 5.8129826E-06 7.6556206E-04 at 50iterations finished qdiffx linear iterations at : 19:37:15 total time elapsed so far: 4.340000 # loops : 50 mean,max change (kT/e) : 5.8129826E-06 7.6556206E-04 energy calculations done at 4.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.500000 DelPhi exited at 19:37:16 4.504u 0.385s 0:05.42 90.0% 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 19:37:16 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2665 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.685048 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): -9.447001 40.28000 ymin,ymax (A): -9.684999 40.89100 zmin,zma (A): -0.8190000 62.56200 x,y,z range (A): 49.72700 50.57600 63.38100 scale (grids/A): 1.685048 object centre (A): 15.41650 15.60300 30.87150 number of atom coordinates read : 2665 total number of charged atoms : 2528 net assigned charge : 4.500024 assigned positive charge : 390.9908 centred at (gu) : 91.29101 88.35020 87.95654 assigned negative charge : -386.4918 centred at (gu) : 90.97292 87.95837 88.00719 start vw surface at 0.1200000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 63128 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26354 grid for indexing accessible points = 1.400000 m= 20212 mr = 41560 m= 2407 mr = 13788 m= 93 mr = 1244 m= 1 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 172 time to turn everything in is 0.5200000 number of dielectric boundary points 29231 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 277 iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 19521 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) : 0.5616825 object centre at (A) : 15.41650 15.60300 30.87150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.3324462E-02 2.1622619E-02 midg,1,midg; midg,igrid,midg -7.8720162E-03 8.1324298E-03 1,midg,midg; igrid,midg,midg -4.7053583E-03 7.4070366E-04 gauss-seidel spectral radius is 0.9982864 estimated iterations to convergence 192 setup time was (sec) 0.8400000 now iterating at: 19:37:17 rms-change max change #iterations 3.306244 167.2157 at 10iterations 1.401930 57.90847 at 20iterations 0.5969506 21.30039 at 30iterations 0.2554442 10.42477 at 40iterations 0.1090643 4.567176 at 50iterations 4.6541810E-02 1.653964 at 60iterations 1.9867925E-02 0.8052359 at 70iterations 8.5241525E-03 0.3133545 at 80iterations 3.6359136E-03 0.1338673 at 90iterations 1.5578105E-03 5.5677414E-02 at 100iterations 6.6765054E-04 2.4976730E-02 at 110iterations 2.8567627E-04 1.0167122E-02 at 120iterations finished qdiffx linear iterations at : 19:37:27 total time elapsed so far: 10.79000 # loops : 120 mean,max change (kT/e) : 2.8567627E-04 1.0167122E-02 energy calculations done at 10.79000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.97000 DelPhi exited at 19:37:28 10.970u 0.408s 0:11.88 95.7% 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 19:37:28 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2665 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.527571 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): -9.447001 40.28000 ymin,ymax (A): -9.684999 40.89100 zmin,zma (A): -0.8190000 62.56200 x,y,z range (A): 49.72700 50.57600 63.38100 scale (grids/A): 2.527571 object centre (A): 15.41650 15.60300 30.87150 number of atom coordinates read : 2665 total number of charged atoms : 2528 net assigned charge : 4.500024 assigned positive charge : 390.9908 centred at (gu) : 91.93628 87.52499 86.93468 assigned negative charge : -386.4918 centred at (gu) : 91.45947 86.93752 87.01079 start vw surface at 0.1200000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 146271 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26354 grid for indexing accessible points = 1.400000 m= 68150 mr = 101732 m= 20911 mr = 53356 m= 3925 mr = 15763 m= 335 mr = 2638 m= 7 mr = 159 m= 0 mr = 2 time to grow re-entrant surface = 0.7700000 no. cavity mid-points inaccessible to solvent = 552 time to turn everything in is 1.280000 number of dielectric boundary points 65949 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 16 iepsmp to db, and charging done at 1.410000 number of grid points assigned charge 20208 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) : 1.685048 object centre at (A) : 15.41650 15.60300 30.87150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2488887 0.4727125 midg,1,midg; midg,igrid,midg -7.7369794E-02 0.1157928 1,midg,midg; igrid,midg,midg -6.8027496E-02 -4.6557481E-03 gauss-seidel spectral radius is 0.9991764 estimated iterations to convergence 275 setup time was (sec) 1.600000 now iterating at: 19:37:30 rms-change max change #iterations 8.469605 333.3104 at 10iterations 4.856375 131.2121 at 20iterations 2.747935 67.67623 at 30iterations 1.553040 40.31950 at 40iterations 0.8747193 22.07907 at 50iterations 0.4907366 11.42214 at 60iterations 0.2748140 6.581919 at 70iterations 0.1536931 3.235854 at 80iterations 8.5780181E-02 1.849907 at 90iterations 4.7943387E-02 1.160217 at 100iterations 2.6725650E-02 0.5679479 at 110iterations 1.4919059E-02 0.3156242 at 120iterations 8.3344579E-03 0.1833954 at 130iterations 4.6327566E-03 9.6103668E-02 at 140iterations 2.5811326E-03 5.2680969E-02 at 150iterations 1.4363402E-03 2.8570175E-02 at 160iterations 8.0083159E-04 1.6852379E-02 at 170iterations 4.4529917E-04 8.7471008E-03 at 180iterations finished qdiffx linear iterations at : 19:37:46 total time elapsed so far: 17.85000 # loops : 180 mean,max change (kT/e) : 4.4529917E-04 8.7471008E-03 energy calculations done at 17.85000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.99000 DelPhi exited at 19:37:47 17.997u 0.468s 0:19.11 96.5% 0+0k 0+0io 0pf+0w