Tue Oct 11 08:29:08 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 Tue Oct 11 2011 at 08:29:08 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: 318 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2859 !!! WARNING: GLU 295 has a net charge of -2.0000 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: 0.6396320 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): -4.861000 50.79600 ymin,ymax (A): 9.492001 61.91700 zmin,zma (A): 0.5830001 55.13800 x,y,z range (A): 55.65700 52.42500 54.55500 scale (grids/A): 0.6396320 object centre (A): 22.96750 35.70450 27.86050 number of atom coordinates read : 2859 total number of charged atoms : 2629 net assigned charge : 4.500018 assigned positive charge : 421.4866 centred at (gu) : 89.48273 90.25040 91.21922 assigned negative charge : -416.9872 centred at (gu) : 89.65575 90.15293 91.15235 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7471 nv = 96 ne = 84 npr = 59785 no. pairs analyzed = 59785 no. exposed pairs = 3391 no. arc points = 23973 no. surface atoms = 1157 nbur = 1702 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 449 mr = 4116 m= 0 mr = 71 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 31 time to turn everything in is 0.3400000 number of dielectric boundary points 3733 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2273 ## 259 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 8976 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.5557710E-09 1.8784638E-08 midg,1,midg; midg,igrid,midg -5.6445164E-09 1.9185952E-08 1,midg,midg; igrid,midg,midg 3.0503148E-08 -1.3925565E-08 gauss-seidel spectral radius is 0.9873543 estimated iterations to convergence 73 setup time was (sec) 0.6200000 now iterating at: 08:29:09 rms-change max change #iterations 0.1534180 22.99521 at 10iterations 1.5528108E-02 2.068579 at 20iterations 1.5643936E-03 0.2310085 at 30iterations 1.5958011E-04 2.0889282E-02 at 40iterations 1.7839013E-05 3.2539368E-03 at 50iterations finished qdiffx linear iterations at : 08:29:12 total time elapsed so far: 4.030000 # loops : 50 mean,max change (kT/e) : 1.7839013E-05 3.2539368E-03 energy calculations done at 4.030000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.210000 DelPhi exited at 08:29:13 4.212u 0.237s 0:04.92 90.2% 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 Tue Oct 11 2011 at 08:29:13 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: 318 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2859 !!! WARNING: GLU 295 has a net charge of -2.0000 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: 1.918896 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): -4.861000 50.79600 ymin,ymax (A): 9.492001 61.91700 zmin,zma (A): 0.5830001 55.13800 x,y,z range (A): 55.65700 52.42500 54.55500 scale (grids/A): 1.918896 object centre (A): 22.96750 35.70450 27.86050 number of atom coordinates read : 2859 total number of charged atoms : 2629 net assigned charge : 4.500018 assigned positive charge : 421.4866 centred at (gu) : 88.44749 90.75019 93.65671 assigned negative charge : -416.9872 centred at (gu) : 88.96680 90.45857 93.45665 start vw surface at 0.1600000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 79760 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23973 grid for indexing accessible points = 1.400000 m= 30399 mr = 54936 m= 5497 mr = 22796 m= 373 mr = 3632 m= 5 mr = 150 m= 0 mr = 0 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 2037 time to turn everything in is 0.7200000 number of dielectric boundary points 34520 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 196 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 20689 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) : 0.6396320 object centre at (A) : 22.96750 35.70450 27.86050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.2438172E-02 9.7214349E-02 midg,1,midg; midg,igrid,midg -6.3684070E-03 -9.8674744E-04 1,midg,midg; igrid,midg,midg 6.4397372E-02 -5.8737911E-02 gauss-seidel spectral radius is 0.9986763 estimated iterations to convergence 218 setup time was (sec) 1.040000 now iterating at: 08:29:14 rms-change max change #iterations 4.496378 190.8615 at 10iterations 2.127039 87.72949 at 20iterations 1.010678 29.61707 at 30iterations 0.4806779 17.43383 at 40iterations 0.2272443 6.316162 at 50iterations 0.1079658 3.031038 at 60iterations 5.1079664E-02 1.487903 at 70iterations 2.4362490E-02 0.7484894 at 80iterations 1.1543572E-02 0.3447485 at 90iterations 5.4660956E-03 0.1749344 at 100iterations 2.6121885E-03 8.0242157E-02 at 110iterations 1.2427660E-03 3.7586689E-02 at 120iterations finished qdiffx linear iterations at : 08:29:23 total time elapsed so far: 9.510000 # loops : 120 mean,max change (kT/e) : 1.2427660E-03 3.7586689E-02 energy calculations done at 9.510000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.680000 DelPhi exited at 08:29:23 9.682u 0.287s 0:10.24 97.2% 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 Tue Oct 11 2011 at 08:29:23 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: 318 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2859 !!! WARNING: GLU 295 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.878344 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): -4.861000 50.79600 ymin,ymax (A): 9.492001 61.91700 zmin,zma (A): 0.5830001 55.13800 x,y,z range (A): 55.65700 52.42500 54.55500 scale (grids/A): 2.878344 object centre (A): 22.96750 35.70450 27.86050 number of atom coordinates read : 2859 total number of charged atoms : 2629 net assigned charge : 4.500018 assigned positive charge : 421.4866 centred at (gu) : 87.67107 91.12531 95.48508 assigned negative charge : -416.9872 centred at (gu) : 88.45016 90.68786 95.18488 start vw surface at 0.1900000 fill in re-entrant regions at 0.6100000 boundary points on vw surface= 183920 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23973 grid for indexing accessible points = 1.400000 m= 95429 mr = 132823 m= 37835 mr = 78370 m= 10092 mr = 30857 m= 1632 mr = 7920 m= 104 mr = 1145 m= 1 mr = 53 m= 0 mr = 0 time to grow re-entrant surface = 0.9600000 no. cavity mid-points inaccessible to solvent = 6663 time to turn everything in is 1.720000 number of dielectric boundary points 77845 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.860000 number of grid points assigned charge 21031 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) : 1.918896 object centre at (A) : 22.96750 35.70450 27.86050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2422397 1.385894 midg,1,midg; midg,igrid,midg -2.1217009E-02 -0.1659633 1,midg,midg; igrid,midg,midg 1.116141 -0.7721210 gauss-seidel spectral radius is 0.9992710 estimated iterations to convergence 292 setup time was (sec) 2.050000 now iterating at: 08:29:26 rms-change max change #iterations 10.40292 347.8073 at 10iterations 6.106756 146.0038 at 20iterations 3.566966 86.25916 at 30iterations 2.075408 54.20330 at 40iterations 1.209100 28.55924 at 50iterations 0.7025725 13.56190 at 60iterations 0.4071098 8.697636 at 70iterations 0.2366258 4.558681 at 80iterations 0.1366931 2.723083 at 90iterations 7.9120867E-02 1.658316 at 100iterations 4.6000201E-02 0.8380280 at 110iterations 2.6552556E-02 0.4738426 at 120iterations 1.5341574E-02 0.2765865 at 130iterations 8.8732438E-03 0.1522932 at 140iterations 5.1414063E-03 9.1709137E-02 at 150iterations 2.9799228E-03 5.1551819E-02 at 160iterations 1.7336997E-03 3.1419754E-02 at 170iterations 1.0146202E-03 1.7497063E-02 at 180iterations finished qdiffx linear iterations at : 08:29:39 total time elapsed so far: 15.48000 # loops : 180 mean,max change (kT/e) : 1.0146202E-03 1.7497063E-02 energy calculations done at 15.48000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.66000 DelPhi exited at 08:29:40 15.658u 0.294s 0:16.29 97.8% 0+0k 0+0io 0pf+0w