Sun Oct 9 13:34:43 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 Sun Oct 9 2011 at 13:34:43 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 = 2365 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: 0.6939165 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): -7.051000 44.25000 ymin,ymax (A): -14.18500 37.11800 zmin,zma (A): 1.975000 44.83700 x,y,z range (A): 51.30100 51.30300 42.86200 scale (grids/A): 0.6939165 object centre (A): 18.59950 11.46650 23.40600 number of atom coordinates read : 2365 total number of charged atoms : 2225 net assigned charge : 4.500011 assigned positive charge : 359.3971 centred at (gu) : 89.77364 91.06549 90.78844 assigned negative charge : -354.8976 centred at (gu) : 89.76971 91.20001 90.82039 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7798 nv = 96 ne = 84 npr = 47072 no. pairs analyzed = 47072 no. exposed pairs = 2996 no. arc points = 20945 no. surface atoms = 1003 nbur = 1362 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 486 mr = 4343 m= 2 mr = 62 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3881 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2007 ## 191 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 8753 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.5468489E-08 1.7276770E-08 midg,1,midg; midg,igrid,midg 6.7201285E-08 -3.5386780E-08 1,midg,midg; igrid,midg,midg 2.7752904E-08 2.8546600E-08 gauss-seidel spectral radius is 0.9892110 estimated iterations to convergence 78 setup time was (sec) 0.6100000 now iterating at: 13:34:44 rms-change max change #iterations 0.1974586 25.41370 at 10iterations 2.3622060E-02 3.484030 at 20iterations 3.2031364E-03 0.4805946 at 30iterations 6.1031186E-04 9.6255302E-02 at 40iterations 1.7992413E-04 2.8285980E-02 at 50iterations finished qdiffx linear iterations at : 13:34:48 total time elapsed so far: 3.880000 # loops : 50 mean,max change (kT/e) : 1.7992413E-04 2.8285980E-02 energy calculations done at 3.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.050000 DelPhi exited at 13:34:48 4.053u 0.251s 0:04.63 92.8% 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 Sun Oct 9 2011 at 13:34:48 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2365 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: 2.081749 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): -7.051000 44.25000 ymin,ymax (A): -14.18500 37.11800 zmin,zma (A): 1.975000 44.83700 x,y,z range (A): 51.30100 51.30300 42.86200 scale (grids/A): 2.081749 object centre (A): 18.59950 11.46650 23.40600 number of atom coordinates read : 2365 total number of charged atoms : 2225 net assigned charge : 4.500011 assigned positive charge : 359.3971 centred at (gu) : 89.32059 93.19612 92.36478 assigned negative charge : -354.8976 centred at (gu) : 89.30885 93.59979 92.46088 start vw surface at 0.1500000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 82883 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20945 grid for indexing accessible points = 1.400000 m= 31715 mr = 57718 m= 5853 mr = 23728 m= 602 mr = 3731 m= 9 mr = 344 m= 0 mr = 0 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7400000 number of dielectric boundary points 35541 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 113 iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 17683 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) : 0.6939165 object centre at (A) : 18.59950 11.46650 23.40600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.6814515E-02 1.5258600E-02 midg,1,midg; midg,igrid,midg 1.4480172E-02 -3.0560965E-02 1,midg,midg; igrid,midg,midg 4.6074539E-02 -1.3543198E-02 gauss-seidel spectral radius is 0.9988295 estimated iterations to convergence 231 setup time was (sec) 1.040000 now iterating at: 13:34:49 rms-change max change #iterations 4.853606 238.1165 at 10iterations 2.385656 83.99255 at 20iterations 1.182281 35.49844 at 30iterations 0.5869235 17.04448 at 40iterations 0.2903758 8.535023 at 50iterations 0.1444035 4.705599 at 60iterations 7.1478575E-02 2.203747 at 70iterations 3.5639457E-02 1.146523 at 80iterations 1.7834686E-02 0.5267203 at 90iterations 8.9405160E-03 0.2890892 at 100iterations 4.5574163E-03 0.1415088 at 110iterations 2.3856384E-03 7.3783875E-02 at 120iterations finished qdiffx linear iterations at : 13:34:58 total time elapsed so far: 9.370000 # loops : 120 mean,max change (kT/e) : 2.3856384E-03 7.3783875E-02 energy calculations done at 9.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.550000 DelPhi exited at 13:34:58 9.551u 0.299s 0:10.16 96.8% 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 Sun Oct 9 2011 at 13:34:58 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 = 2365 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: 3.122624 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): -7.051000 44.25000 ymin,ymax (A): -14.18500 37.11800 zmin,zma (A): 1.975000 44.83700 x,y,z range (A): 51.30100 51.30300 42.86200 scale (grids/A): 3.122624 object centre (A): 18.59950 11.46650 23.40600 number of atom coordinates read : 2365 total number of charged atoms : 2225 net assigned charge : 4.500011 assigned positive charge : 359.3971 centred at (gu) : 88.98079 94.79423 93.54705 assigned negative charge : -354.8976 centred at (gu) : 88.96336 95.39960 93.69142 start vw surface at 0.1500000 fill in re-entrant regions at 1.060000 boundary points on vw surface= 191077 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20945 grid for indexing accessible points = 1.400000 m= 100307 mr = 139195 m= 39043 mr = 82455 m= 10786 mr = 31937 m= 2387 mr = 8239 m= 332 mr = 1827 m= 10 mr = 226 m= 0 mr = 0 time to grow re-entrant surface = 1.210000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.400000 number of dielectric boundary points 80063 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.560000 number of grid points assigned charge 17800 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) : 2.081749 object centre at (A) : 18.59950 11.46650 23.40600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3524124 3.4672245E-02 midg,1,midg; midg,igrid,midg 0.2692368 -0.4412207 1,midg,midg; igrid,midg,midg 0.4613501 -0.4518834 gauss-seidel spectral radius is 0.9992986 estimated iterations to convergence 298 setup time was (sec) 2.730000 now iterating at: 13:35:01 rms-change max change #iterations 10.76515 406.6611 at 10iterations 6.382924 128.5565 at 20iterations 3.766292 78.10857 at 30iterations 2.229539 44.31907 at 40iterations 1.313271 23.80503 at 50iterations 0.7718741 13.22237 at 60iterations 0.4542505 7.918700 at 70iterations 0.2660609 4.676338 at 80iterations 0.1562224 2.485264 at 90iterations 9.1647007E-02 1.595792 at 100iterations 5.3804565E-02 0.9315262 at 110iterations 3.1715397E-02 0.5651512 at 120iterations 1.8872524E-02 0.3355103 at 130iterations 1.1338296E-02 0.1973610 at 140iterations 6.9885193E-03 0.1322060 at 150iterations 4.4905636E-03 9.7244263E-02 at 160iterations 3.0577451E-03 6.6841125E-02 at 170iterations 2.2150299E-03 4.7584057E-02 at 180iterations finished qdiffx linear iterations at : 13:35:15 total time elapsed so far: 16.55000 # loops : 180 mean,max change (kT/e) : 2.2150299E-03 4.7584057E-02 energy calculations done at 16.55000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.73000 DelPhi exited at 13:35:16 16.731u 0.318s 0:17.31 98.4% 0+0k 0+0io 0pf+0w