Mon Oct 10 19:43:48 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 19:43:48 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2800 !!! WARNING: GLM 817 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6197664 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): -32.23800 25.20300 ymin,ymax (A): 29.11200 82.65700 zmin,zma (A): 60.40100 108.6180 x,y,z range (A): 57.44100 53.54500 48.21701 scale (grids/A): 0.6197664 object centre (A): -3.517500 55.88450 84.50950 number of atom coordinates read : 2800 total number of charged atoms : 2655 net assigned charge : 2.906025 assigned positive charge : 422.2256 centred at (gu) : 88.49115 91.84672 90.16336 assigned negative charge : -419.3206 centred at (gu) : 88.56105 91.88908 90.19860 start vw surface at 0.1500000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7005 nv = 96 ne = 84 npr = 58120 no. pairs analyzed = 58120 no. exposed pairs = 3466 no. arc points = 24432 no. surface atoms = 1167 nbur = 1633 mkacc time = 0.1900000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 365 mr = 3759 m= 0 mr = 32 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 6 time to turn everything in is 0.4000000 number of dielectric boundary points 3579 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2442 ## 219 charges are in solution ## iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 8669 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.6137778E-09 -2.2699470E-10 midg,1,midg; midg,igrid,midg 3.5383767E-09 -1.1793794E-09 1,midg,midg; igrid,midg,midg 1.0091626E-08 -1.9003688E-09 gauss-seidel spectral radius is 0.9865332 estimated iterations to convergence 71 setup time was (sec) 0.7400000 now iterating at: 19:43:49 rms-change max change #iterations 0.1298901 19.04718 at 10iterations 1.1872439E-02 1.666538 at 20iterations 1.0957486E-03 0.1489143 at 30iterations 1.0122945E-04 1.4953613E-02 at 40iterations 9.9767731E-06 1.4550686E-03 at 50iterations finished qdiffx linear iterations at : 19:43:53 total time elapsed so far: 4.610000 # loops : 50 mean,max change (kT/e) : 9.9767731E-06 1.4550686E-03 energy calculations done at 4.610000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.830000 DelPhi exited at 19:43:54 4.831u 0.413s 0:05.83 89.8% 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 Mon Oct 10 2011 at 19:43:54 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2800 !!! WARNING: GLM 817 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.859299 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): -32.23800 25.20300 ymin,ymax (A): 29.11200 82.65700 zmin,zma (A): 60.40100 108.6180 x,y,z range (A): 57.44100 53.54500 48.21701 scale (grids/A): 1.859299 object centre (A): -3.517500 55.88450 84.50950 number of atom coordinates read : 2800 total number of charged atoms : 2655 net assigned charge : 2.906025 assigned positive charge : 422.2256 centred at (gu) : 85.47270 95.53952 90.48949 assigned negative charge : -419.3206 centred at (gu) : 85.68295 95.66673 90.59547 start vw surface at 0.1600000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 75618 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24432 grid for indexing accessible points = 1.400000 m= 26806 mr = 51956 m= 4440 mr = 19264 m= 305 mr = 2662 m= 6 mr = 103 m= 0 mr = 0 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 316 time to turn everything in is 0.7800000 number of dielectric boundary points 33190 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 184 iepsmp to db, and charging done at 0.9100000 number of grid points assigned charge 20821 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) : 0.6197664 object centre at (A) : -3.517500 55.88450 84.50950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.5844984E-03 6.6825803E-03 midg,1,midg; midg,igrid,midg 1.1762459E-02 -6.1665718E-03 1,midg,midg; igrid,midg,midg 1.4154123E-02 7.0704548E-03 gauss-seidel spectral radius is 0.9985852 estimated iterations to convergence 211 setup time was (sec) 1.110000 now iterating at: 19:43:55 rms-change max change #iterations 4.240020 171.6344 at 10iterations 1.956671 78.38157 at 20iterations 0.9013979 30.36455 at 30iterations 0.4182239 13.01054 at 40iterations 0.1932694 6.304806 at 50iterations 8.9215361E-02 3.148216 at 60iterations 4.1267596E-02 1.401806 at 70iterations 1.9082237E-02 0.6034050 at 80iterations 8.8204714E-03 0.2962284 at 90iterations 4.0759756E-03 0.1335754 at 100iterations 1.8896096E-03 5.9165955E-02 at 110iterations 8.7201170E-04 2.6250362E-02 at 120iterations finished qdiffx linear iterations at : 19:44:05 total time elapsed so far: 10.81000 # loops : 120 mean,max change (kT/e) : 8.7201170E-04 2.6250362E-02 energy calculations done at 10.81000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.03000 DelPhi exited at 19:44:06 11.033u 0.468s 0:11.80 97.3% 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 19:44:06 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2800 !!! WARNING: GLM 817 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.788949 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): -32.23800 25.20300 ymin,ymax (A): 29.11200 82.65700 zmin,zma (A): 60.40100 108.6180 x,y,z range (A): 57.44100 53.54500 48.21701 scale (grids/A): 2.788949 object centre (A): -3.517500 55.88450 84.50950 number of atom coordinates read : 2800 total number of charged atoms : 2655 net assigned charge : 2.906025 assigned positive charge : 422.2256 centred at (gu) : 83.20901 98.30916 90.73397 assigned negative charge : -419.3206 centred at (gu) : 83.52445 98.49999 90.89314 start vw surface at 0.1800000 fill in re-entrant regions at 0.6800000 boundary points on vw surface= 175572 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24432 grid for indexing accessible points = 1.400000 m= 85895 mr = 126833 m= 31568 mr = 69088 m= 7897 mr = 24770 m= 1149 mr = 5749 m= 59 mr = 727 m= 2 mr = 19 m= 0 mr = 0 time to grow re-entrant surface = 1.220000 no. cavity mid-points inaccessible to solvent = 1071 time to turn everything in is 2.040000 number of dielectric boundary points 74956 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 2.210000 number of grid points assigned charge 21240 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) : 1.859299 object centre at (A) : -3.517500 55.88450 84.50950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.9073938E-02 5.9338480E-02 midg,1,midg; midg,igrid,midg 0.1974340 -0.1356582 1,midg,midg; igrid,midg,midg 9.2489764E-02 6.7627646E-02 gauss-seidel spectral radius is 0.9992512 estimated iterations to convergence 288 setup time was (sec) 2.420000 now iterating at: 19:44:09 rms-change max change #iterations 10.01861 368.0743 at 10iterations 5.832276 120.3946 at 20iterations 3.377984 88.85765 at 30iterations 1.942973 38.84374 at 40iterations 1.118966 21.94889 at 50iterations 0.6429958 11.60780 at 60iterations 0.3688751 6.723711 at 70iterations 0.2122262 3.860863 at 80iterations 0.1217529 2.157807 at 90iterations 6.9778182E-02 1.367761 at 100iterations 3.9920051E-02 0.7229595 at 110iterations 2.2859231E-02 0.4160480 at 120iterations 1.3102882E-02 0.2314663 at 130iterations 7.5000939E-03 0.1385384 at 140iterations 4.3017021E-03 7.6217651E-02 at 150iterations 2.4614232E-03 4.4324636E-02 at 160iterations 1.4117277E-03 2.6129246E-02 at 170iterations 8.0987607E-04 1.5159845E-02 at 180iterations finished qdiffx linear iterations at : 19:44:25 total time elapsed so far: 18.70000 # loops : 180 mean,max change (kT/e) : 8.0987607E-04 1.5159845E-02 energy calculations done at 18.70000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.92000 DelPhi exited at 19:44:26 18.920u 0.455s 0:19.74 98.1% 0+0k 0+0io 0pf+0w