Tue Oct 11 06:09:37 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 Tue Oct 11 2011 at 06:09:38 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2040 !!! WARNING: SEP 190 has a net charge of -0.4750 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: 0.7195408 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): 3.574000 46.49900 ymin,ymax (A): 0.5849999 40.25900 zmin,zma (A): -2.153000 47.32300 x,y,z range (A): 42.92500 39.67400 49.47600 scale (grids/A): 0.7195408 object centre (A): 25.03650 20.42200 22.58500 number of atom coordinates read : 2040 total number of charged atoms : 1910 net assigned charge : 7.025009 assigned positive charge : 310.6992 centred at (gu) : 90.26340 90.53252 90.17693 assigned negative charge : -303.6742 centred at (gu) : 90.45625 90.49873 90.20132 start vw surface at 0.1700000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7150 nv = 96 ne = 84 npr = 41067 no. pairs analyzed = 41067 no. exposed pairs = 2478 no. arc points = 16783 no. surface atoms = 846 nbur = 1194 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 484 mr = 4125 m= 3 mr = 94 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 3418 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1581 ## 136 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 7810 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.1137942E-08 6.5664629E-08 midg,1,midg; midg,igrid,midg 5.2378347E-08 1.1060481E-07 1,midg,midg; igrid,midg,midg 1.8796277E-07 -4.7073971E-08 gauss-seidel spectral radius is 0.9899231 estimated iterations to convergence 81 setup time was (sec) 0.6300000 now iterating at: 06:09:38 rms-change max change #iterations 0.2152929 31.57334 at 10iterations 2.8094091E-02 3.781502 at 20iterations 3.7493438E-03 0.5384245 at 30iterations 6.1330304E-04 7.8899384E-02 at 40iterations 1.5463705E-04 2.3178101E-02 at 50iterations finished qdiffx linear iterations at : 06:09:42 total time elapsed so far: 4.050000 # loops : 50 mean,max change (kT/e) : 1.5463705E-04 2.3178101E-02 energy calculations done at 4.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.240000 DelPhi exited at 06:09:42 4.239u 0.247s 0:04.84 92.3% 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 Tue Oct 11 2011 at 06:09:42 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2040 !!! WARNING: SEP 190 has a net charge of -0.4750 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: 2.158622 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): 3.574000 46.49900 ymin,ymax (A): 0.5849999 40.25900 zmin,zma (A): -2.153000 47.32300 x,y,z range (A): 42.92500 39.67400 49.47600 scale (grids/A): 2.158622 object centre (A): 25.03650 20.42200 22.58500 number of atom coordinates read : 2040 total number of charged atoms : 1910 net assigned charge : 7.025009 assigned positive charge : 310.6992 centred at (gu) : 90.79038 91.59787 90.53095 assigned negative charge : -303.6742 centred at (gu) : 91.36902 91.49623 90.60397 start vw surface at 0.1700000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 76175 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16783 grid for indexing accessible points = 1.400000 m= 30972 mr = 54451 m= 6089 mr = 23763 m= 576 mr = 4113 m= 14 mr = 286 m= 0 mr = 3 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6700000 number of dielectric boundary points 31210 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 59 iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 15172 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) : 0.7195408 object centre at (A) : 25.03650 20.42200 22.58500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.2869013E-02 6.0116395E-02 midg,1,midg; midg,igrid,midg 4.4122147E-03 3.4986518E-02 1,midg,midg; igrid,midg,midg 4.8354141E-02 -1.7332719E-03 gauss-seidel spectral radius is 0.9988589 estimated iterations to convergence 234 setup time was (sec) 1.000000 now iterating at: 06:09:44 rms-change max change #iterations 4.704497 251.8740 at 10iterations 2.349227 96.59039 at 20iterations 1.178718 37.79170 at 30iterations 0.5913834 18.25622 at 40iterations 0.2965071 8.463019 at 50iterations 0.1491934 4.941283 at 60iterations 7.4463531E-02 2.151246 at 70iterations 3.7521243E-02 1.283328 at 80iterations 1.8839391E-02 0.5288845 at 90iterations 9.5480001E-03 0.2823439 at 100iterations 4.8467852E-03 0.1532364 at 110iterations 2.5108729E-03 7.3574066E-02 at 120iterations finished qdiffx linear iterations at : 06:09:52 total time elapsed so far: 9.550000 # loops : 120 mean,max change (kT/e) : 2.5108729E-03 7.3574066E-02 energy calculations done at 9.550000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.720000 DelPhi exited at 06:09:53 9.727u 0.282s 0:10.34 96.7% 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 Tue Oct 11 2011 at 06:09:53 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2040 !!! WARNING: SEP 190 has a net charge of -0.4750 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: 3.237933 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): 3.574000 46.49900 ymin,ymax (A): 0.5849999 40.25900 zmin,zma (A): -2.153000 47.32300 x,y,z range (A): 42.92500 39.67400 49.47600 scale (grids/A): 3.237933 object centre (A): 25.03650 20.42200 22.58500 number of atom coordinates read : 2040 total number of charged atoms : 1910 net assigned charge : 7.025009 assigned positive charge : 310.6992 centred at (gu) : 91.18554 92.39677 90.79638 assigned negative charge : -303.6742 centred at (gu) : 92.05351 92.24435 90.90597 start vw surface at 0.1500000 fill in re-entrant regions at 0.9100000 boundary points on vw surface= 175501 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16783 grid for indexing accessible points = 1.400000 m= 96302 mr = 130929 m= 39720 mr = 80581 m= 11783 mr = 33007 m= 2438 mr = 9167 m= 267 mr = 1783 m= 7 mr = 185 m= 0 mr = 2 time to grow re-entrant surface = 0.9900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.010000 number of dielectric boundary points 70364 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.150000 number of grid points assigned charge 15280 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) : 2.158622 object centre at (A) : 25.03650 20.42200 22.58500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3628291 0.6467690 midg,1,midg; midg,igrid,midg -4.2215148E-03 0.2494346 1,midg,midg; igrid,midg,midg 0.3469757 6.0396589E-02 gauss-seidel spectral radius is 0.9993005 estimated iterations to convergence 298 setup time was (sec) 2.350000 now iterating at: 06:09:55 rms-change max change #iterations 10.39793 304.3250 at 10iterations 6.164908 157.1513 at 20iterations 3.646022 71.38500 at 30iterations 2.157053 45.49346 at 40iterations 1.272545 26.57143 at 50iterations 0.7499858 15.06987 at 60iterations 0.4414520 7.858500 at 70iterations 0.2592162 5.109828 at 80iterations 0.1525065 2.546127 at 90iterations 8.9870900E-02 1.574336 at 100iterations 5.2803334E-02 1.055043 at 110iterations 3.1128109E-02 0.5861816 at 120iterations 1.8496424E-02 0.3342199 at 130iterations 1.1118729E-02 0.1953011 at 140iterations 6.8210969E-03 0.1391411 at 150iterations 4.3195249E-03 8.0970764E-02 at 160iterations 2.8705606E-03 5.1219940E-02 at 170iterations 2.0192452E-03 3.8028717E-02 at 180iterations finished qdiffx linear iterations at : 06:10:09 total time elapsed so far: 16.02000 # loops : 180 mean,max change (kT/e) : 2.0192452E-03 3.8028717E-02 energy calculations done at 16.02000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.19000 DelPhi exited at 06:10:10 16.193u 0.291s 0:17.13 96.2% 0+0k 0+0io 0pf+0w