Sat Oct 15 11:27:39 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 Sat Oct 15 2011 at 11:27:39 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3444 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: 0.5565283 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): -2.022000 53.59300 ymin,ymax (A): -19.51400 39.28300 zmin,zma (A): -5.264000 58.70400 x,y,z range (A): 55.61500 58.79700 63.96800 scale (grids/A): 0.5565283 object centre (A): 25.78550 9.884501 26.72000 number of atom coordinates read : 3444 total number of charged atoms : 3298 net assigned charge : -5.999964 assigned positive charge : 514.3504 centred at (gu) : 89.87465 87.71498 89.82204 assigned negative charge : -520.3519 centred at (gu) : 89.91672 87.69208 89.83842 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7015 nv = 96 ne = 84 npr = 69309 no. pairs analyzed = 69309 no. exposed pairs = 4491 no. arc points = 31407 no. surface atoms = 1494 nbur = 1950 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 277 mr = 3614 m= 0 mr = 3 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2400000 number of dielectric boundary points 3675 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3212 ## 395 charges are in solution ## iepsmp to db, and charging done at 0.3300000 number of grid points assigned charge 9171 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.8025308E-10 -7.0740025E-10 midg,1,midg; midg,igrid,midg -1.4152443E-09 -1.7519418E-10 1,midg,midg; igrid,midg,midg -7.6359516E-11 -1.0017537E-09 gauss-seidel spectral radius is 0.9833872 estimated iterations to convergence 64 setup time was (sec) 0.4800000 now iterating at: 11:27:40 rms-change max change #iterations 8.5904330E-02 12.92072 at 10iterations 6.1118440E-03 1.017559 at 20iterations 5.4454780E-04 7.3894501E-02 at 30iterations 1.0306799E-04 1.5561104E-02 at 40iterations 2.9514380E-05 4.4364929E-03 at 50iterations finished qdiffx linear iterations at : 11:27:43 total time elapsed so far: 3.840000 # loops : 50 mean,max change (kT/e) : 2.9514380E-05 4.4364929E-03 energy calculations done at 3.840000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.970000 DelPhi exited at 11:27:44 3.977u 0.253s 0:04.56 92.5% 0+0k 0+0io 6pf+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 Sat Oct 15 2011 at 11:27:44 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 = 3444 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: 1.669585 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): -2.022000 53.59300 ymin,ymax (A): -19.51400 39.28300 zmin,zma (A): -5.264000 58.70400 x,y,z range (A): 55.61500 58.79700 63.96800 scale (grids/A): 1.669585 object centre (A): 25.78550 9.884501 26.72000 number of atom coordinates read : 3444 total number of charged atoms : 3298 net assigned charge : -5.999964 assigned positive charge : 514.3504 centred at (gu) : 89.62320 83.14409 89.46492 assigned negative charge : -520.3519 centred at (gu) : 89.74982 83.07577 89.51492 start vw surface at 0.1000000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 77463 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31407 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 24447 mr = 52678 m= 2541 mr = 16576 m= 76 mr = 1149 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 404 time to turn everything in is 0.4000000 number of dielectric boundary points 34124 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 366 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 25454 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) : 0.5565283 object centre at (A) : 25.78550 9.884501 26.72000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.4275174E-03 -2.2800254E-02 midg,1,midg; midg,igrid,midg -1.6785301E-02 1.0426320E-03 1,midg,midg; igrid,midg,midg -8.0893347E-03 -3.1885829E-02 gauss-seidel spectral radius is 0.9983167 estimated iterations to convergence 193 setup time was (sec) 0.6800000 now iterating at: 11:27:45 rms-change max change #iterations 3.779916 157.7252 at 10iterations 1.614469 56.50959 at 20iterations 0.6974878 23.22736 at 30iterations 0.3003229 10.40322 at 40iterations 0.1289799 4.873329 at 50iterations 5.5655245E-02 1.780071 at 60iterations 2.3953501E-02 0.7730808 at 70iterations 1.0331134E-02 0.3829017 at 80iterations 4.4917115E-03 0.1431351 at 90iterations 1.9466896E-03 6.5350056E-02 at 100iterations 8.5401552E-04 2.9476166E-02 at 110iterations 3.8326706E-04 1.4890671E-02 at 120iterations finished qdiffx linear iterations at : 11:27:53 total time elapsed so far: 9.150000 # loops : 120 mean,max change (kT/e) : 3.8326706E-04 1.4890671E-02 energy calculations done at 9.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.280000 DelPhi exited at 11:27:54 9.287u 0.319s 0:09.98 96.0% 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 Sat Oct 15 2011 at 11:27:54 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3444 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: 2.504377 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): -2.022000 53.59300 ymin,ymax (A): -19.51400 39.28300 zmin,zma (A): -5.264000 58.70400 x,y,z range (A): 55.61500 58.79700 63.96800 scale (grids/A): 2.504377 object centre (A): 25.78550 9.884501 26.72000 number of atom coordinates read : 3444 total number of charged atoms : 3298 net assigned charge : -5.999964 assigned positive charge : 514.3504 centred at (gu) : 89.43478 79.71597 89.19732 assigned negative charge : -520.3519 centred at (gu) : 89.62446 79.61353 89.27237 start vw surface at 0.1000000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 179705 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31407 grid for indexing accessible points = 1.400000 m= 84400 mr = 128665 m= 24322 mr = 66487 m= 3975 mr = 17922 m= 269 mr = 2420 m= 9 mr = 75 m= 0 mr = 0 time to grow re-entrant surface = 0.5500000 no. cavity mid-points inaccessible to solvent = 1269 time to turn everything in is 0.9800000 number of dielectric boundary points 77111 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 17 iepsmp to db, and charging done at 1.090000 number of grid points assigned charge 26365 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) : 1.669585 object centre at (A) : 25.78550 9.884501 26.72000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.9369073E-03 -0.2501069 midg,1,midg; midg,igrid,midg -0.2230329 1.5690707E-02 1,midg,midg; igrid,midg,midg -0.1512665 -0.5746116 gauss-seidel spectral radius is 0.9991895 estimated iterations to convergence 277 setup time was (sec) 1.250000 now iterating at: 11:27:55 rms-change max change #iterations 9.660661 315.3565 at 10iterations 5.520270 137.4313 at 20iterations 3.147162 64.01557 at 30iterations 1.784214 35.03716 at 40iterations 1.007740 19.43686 at 50iterations 0.5691451 11.10273 at 60iterations 0.3201182 6.506438 at 70iterations 0.1804298 3.507286 at 80iterations 0.1012826 1.802649 at 90iterations 5.6758624E-02 1.149536 at 100iterations 3.1815663E-02 0.5819664 at 110iterations 1.7874751E-02 0.3218184 at 120iterations 1.0003111E-02 0.1974621 at 130iterations 5.6263856E-03 0.1222751 at 140iterations 3.1658162E-03 6.0335159E-02 at 150iterations 1.7852184E-03 3.6405444E-02 at 160iterations 1.0171970E-03 2.0950317E-02 at 170iterations 5.8598729E-04 1.1038780E-02 at 180iterations finished qdiffx linear iterations at : 11:28:09 total time elapsed so far: 15.02000 # loops : 180 mean,max change (kT/e) : 5.8598729E-04 1.1038780E-02 energy calculations done at 15.02000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.16000 DelPhi exited at 11:28:10 15.161u 0.345s 0:16.42 94.3% 0+0k 0+0io 0pf+0w