Tue Oct 11 03:21:26 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 03:21:26 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: 227 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1155 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.7461591 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): -6.678000 29.35700 ymin,ymax (A): 1.330000 40.36900 zmin,zma (A): -1.473000 46.23800 x,y,z range (A): 36.03500 39.03900 47.71100 scale (grids/A): 0.7461591 object centre (A): 11.33950 20.84950 22.38250 number of atom coordinates read : 1155 total number of charged atoms : 1061 net assigned charge : 5.500003 assigned positive charge : 175.3231 centred at (gu) : 89.65716 89.10265 88.42251 assigned negative charge : -169.8232 centred at (gu) : 89.36047 89.07852 88.44227 start vw surface at 5.9999999E-02 fill in re-entrant regions at 5.9999999E-02 boundary points on vw surface= 4390 nv = 96 ne = 84 npr = 22192 no. pairs analyzed = 22192 no. exposed pairs = 1498 no. arc points = 10937 no. surface atoms = 506 nbur = 649 mkacc time = 4.0000003E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 287 mr = 2222 m= 1 mr = 62 m= 0 mr = 0 time to grow re-entrant surface = 5.0000001E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1100000 number of dielectric boundary points 2394 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 944 ## 75 charges are in solution ## iepsmp to db, and charging done at 0.1700000 number of grid points assigned charge 4538 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.6417336E-07 7.5194357E-08 midg,1,midg; midg,igrid,midg 1.1325452E-07 1.0721002E-07 1,midg,midg; igrid,midg,midg -8.0034162E-08 2.6913008E-07 gauss-seidel spectral radius is 0.9905419 estimated iterations to convergence 84 setup time was (sec) 0.2800000 now iterating at: 03:21:26 rms-change max change #iterations 0.1808816 30.99562 at 10iterations 2.4013044E-02 3.636801 at 20iterations 3.1906436E-03 0.5166969 at 30iterations 4.2967161E-04 6.8260193E-02 at 40iterations 5.8356552E-05 9.4280243E-03 at 50iterations finished qdiffx linear iterations at : 03:21:29 total time elapsed so far: 3.090000 # loops : 50 mean,max change (kT/e) : 5.8356552E-05 9.4280243E-03 energy calculations done at 3.090000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.220000 DelPhi exited at 03:21:30 3.225u 0.172s 0:03.74 90.6% 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 03:21:30 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: 227 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1155 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.238477 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): -6.678000 29.35700 ymin,ymax (A): 1.330000 40.36900 zmin,zma (A): -1.473000 46.23800 x,y,z range (A): 36.03500 39.03900 47.71100 scale (grids/A): 2.238477 object centre (A): 11.33950 20.84950 22.38250 number of atom coordinates read : 1155 total number of charged atoms : 1061 net assigned charge : 5.500003 assigned positive charge : 175.3231 centred at (gu) : 88.97159 87.30795 85.26765 assigned negative charge : -169.8232 centred at (gu) : 88.08170 87.23591 85.32698 start vw surface at 5.9999999E-02 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 45740 reading accessible surface arcs data from file ARCDAT no. of arc points read = 10937 grid for indexing accessible points = 1.400000 m= 17203 mr = 29722 m= 3476 mr = 12748 m= 365 mr = 2327 m= 18 mr = 223 m= 0 mr = 13 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2500000 number of dielectric boundary points 21769 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 38 iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 8461 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) : 0.7461591 object centre at (A) : 11.33950 20.84950 22.38250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.7813824E-02 8.5661821E-03 midg,1,midg; midg,igrid,midg 4.3872431E-02 3.6704864E-02 1,midg,midg; igrid,midg,midg -2.5141610E-02 3.9757080E-02 gauss-seidel spectral radius is 0.9988491 estimated iterations to convergence 233 setup time was (sec) 0.4500000 now iterating at: 03:21:30 rms-change max change #iterations 3.634769 180.4115 at 10iterations 1.812738 95.72572 at 20iterations 0.9047546 32.95409 at 30iterations 0.4494150 17.46497 at 40iterations 0.2233636 8.164032 at 50iterations 0.1106976 4.298538 at 60iterations 5.4985270E-02 2.207994 at 70iterations 2.7397765E-02 1.027825 at 80iterations 1.3632516E-02 0.4812927 at 90iterations 6.7491163E-03 0.2460628 at 100iterations 3.3475915E-03 0.1343999 at 110iterations 1.6634482E-03 6.2250137E-02 at 120iterations finished qdiffx linear iterations at : 03:21:38 total time elapsed so far: 8.110000 # loops : 120 mean,max change (kT/e) : 1.6634482E-03 6.2250137E-02 energy calculations done at 8.110000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.230000 DelPhi exited at 03:21:39 8.236u 0.205s 0:08.83 95.4% 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 03:21:39 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: 227 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1155 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.357716 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): -6.678000 29.35700 ymin,ymax (A): 1.330000 40.36900 zmin,zma (A): -1.473000 46.23800 x,y,z range (A): 36.03500 39.03900 47.71100 scale (grids/A): 3.357716 object centre (A): 11.33950 20.84950 22.38250 number of atom coordinates read : 1155 total number of charged atoms : 1061 net assigned charge : 5.500003 assigned positive charge : 175.3231 centred at (gu) : 88.45734 85.96190 82.90147 assigned negative charge : -169.8232 centred at (gu) : 87.12257 85.85394 82.99055 start vw surface at 5.0000001E-02 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 105544 reading accessible surface arcs data from file ARCDAT no. of arc points read = 10937 grid for indexing accessible points = 1.400000 m= 53104 mr = 72070 m= 21798 mr = 43080 m= 6561 mr = 17875 m= 1409 mr = 5179 m= 229 mr = 1107 m= 26 mr = 166 m= 4 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7100000 number of dielectric boundary points 49173 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 8488 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) : 2.238477 object centre at (A) : 11.33950 20.84950 22.38250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2258276 5.3953722E-02 midg,1,midg; midg,igrid,midg 0.3940269 0.3203645 1,midg,midg; igrid,midg,midg -0.1956185 0.2720791 gauss-seidel spectral radius is 0.9992968 estimated iterations to convergence 298 setup time was (sec) 0.9400000 now iterating at: 03:21:40 rms-change max change #iterations 7.952733 404.4085 at 10iterations 4.636249 127.6012 at 20iterations 2.691692 73.09186 at 30iterations 1.553750 35.05521 at 40iterations 0.9050671 20.13464 at 50iterations 0.5247223 11.63210 at 60iterations 0.3053351 6.344219 at 70iterations 0.1765918 3.656969 at 80iterations 0.1025351 2.089538 at 90iterations 5.9523493E-02 1.449112 at 100iterations 3.4449037E-02 0.7378216 at 110iterations 2.0095726E-02 0.5024705 at 120iterations 1.1652461E-02 0.2299023 at 130iterations 6.7573967E-03 0.1559563 at 140iterations 3.9208992E-03 8.5826874E-02 at 150iterations 2.2772010E-03 4.8364878E-02 at 160iterations 1.3202321E-03 2.8461456E-02 at 170iterations 7.6674251E-04 1.6836166E-02 at 180iterations finished qdiffx linear iterations at : 03:21:51 total time elapsed so far: 11.94000 # loops : 180 mean,max change (kT/e) : 7.6674251E-04 1.6836166E-02 energy calculations done at 11.94000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.07000 DelPhi exited at 03:21:51 12.076u 0.243s 0:12.77 96.3% 0+0k 0+0io 0pf+0w