Mon Oct 10 17:03:23 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 Mon Oct 10 2011 at 17:03:23 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2741 !!! WARNING: ASN 14 has a net charge of -0.2720 !!! WARNING: GLY 31 has a net charge of -0.2720 !!! WARNING: HIT 107 has a net charge of 0.5140 !!! WARNING: GLY 170 has a net charge of -0.2720 !!! WARNING: LEU 353 has a net charge of -0.2720 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: 0.6279435 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): 14.42800 71.12100 ymin,ymax (A): 3.787000 50.60200 zmin,zma (A): 6.807000 61.46400 x,y,z range (A): 56.69300 46.81500 54.65700 scale (grids/A): 0.6279435 object centre (A): 42.77450 27.19450 34.13550 number of atom coordinates read : 2741 total number of charged atoms : 2602 net assigned charge : -3.573964 assigned positive charge : 410.9764 centred at (gu) : 89.03204 90.82948 91.52326 assigned negative charge : -414.5514 centred at (gu) : 88.94706 90.97933 91.61166 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7344 nv = 96 ne = 84 npr = 54805 no. pairs analyzed = 54805 no. exposed pairs = 3542 no. arc points = 25187 no. surface atoms = 1194 nbur = 1547 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 364 mr = 3872 m= 1 mr = 51 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 3786 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2506 ## 244 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 8921 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.1599510E-09 -1.5670546E-08 midg,1,midg; midg,igrid,midg 8.1236031E-09 -2.0176008E-08 1,midg,midg; igrid,midg,midg -1.3472496E-08 3.3466390E-09 gauss-seidel spectral radius is 0.9868841 estimated iterations to convergence 71 setup time was (sec) 0.3900000 now iterating at: 17:03:24 rms-change max change #iterations 0.1362811 19.50617 at 10iterations 1.3168466E-02 1.724245 at 20iterations 1.2430372E-03 0.1720715 at 30iterations 1.1875184E-04 1.9001007E-02 at 40iterations 1.1866809E-05 1.5563965E-03 at 50iterations finished qdiffx linear iterations at : 17:03:27 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 1.1866809E-05 1.5563965E-03 energy calculations done at 3.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.350000 DelPhi exited at 17:03:28 3.352u 0.175s 0:04.48 78.5% 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 Mon Oct 10 2011 at 17:03:28 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2741 !!! WARNING: ASN 14 has a net charge of -0.2720 !!! WARNING: GLY 31 has a net charge of -0.2720 !!! WARNING: HIT 107 has a net charge of 0.5140 !!! WARNING: GLY 170 has a net charge of -0.2720 !!! WARNING: LEU 353 has a net charge of -0.2720 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: 1.883830 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): 14.42800 71.12100 ymin,ymax (A): 3.787000 50.60200 zmin,zma (A): 6.807000 61.46400 x,y,z range (A): 56.69300 46.81500 54.65700 scale (grids/A): 1.883830 object centre (A): 42.77450 27.19450 34.13550 number of atom coordinates read : 2741 total number of charged atoms : 2602 net assigned charge : -3.573964 assigned positive charge : 410.9764 centred at (gu) : 87.09546 92.48764 94.56895 assigned negative charge : -414.5514 centred at (gu) : 86.84083 92.93771 94.83482 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 79572 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25187 grid for indexing accessible points = 1.400000 m= 27265 mr = 54139 m= 3902 mr = 19569 m= 185 mr = 2326 m= 2 mr = 71 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 790 time to turn everything in is 0.3700000 number of dielectric boundary points 34821 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 204 iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 20422 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) : 0.6279435 object centre at (A) : 42.77450 27.19450 34.13550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.1115393E-02 8.9388620E-04 midg,1,midg; midg,igrid,midg 1.1769081E-02 -3.2871954E-02 1,midg,midg; igrid,midg,midg -4.8461314E-02 2.4718896E-02 gauss-seidel spectral radius is 0.9986226 estimated iterations to convergence 214 setup time was (sec) 0.5900000 now iterating at: 17:03:29 rms-change max change #iterations 4.331681 184.4093 at 10iterations 2.014147 75.30348 at 20iterations 0.9387914 38.03994 at 30iterations 0.4389907 13.70108 at 40iterations 0.2042023 6.579915 at 50iterations 9.5219024E-02 2.851003 at 60iterations 4.4499144E-02 1.315189 at 70iterations 2.0750497E-02 0.6901836 at 80iterations 9.6701384E-03 0.3324375 at 90iterations 4.5093722E-03 0.1340866 at 100iterations 2.1002349E-03 6.2633038E-02 at 110iterations 9.8165718E-04 3.6140442E-02 at 120iterations finished qdiffx linear iterations at : 17:03:36 total time elapsed so far: 7.570000 # loops : 120 mean,max change (kT/e) : 9.8165718E-04 3.6140442E-02 energy calculations done at 7.570000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.700000 DelPhi exited at 17:03:37 7.705u 0.204s 0:09.14 86.4% 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 Mon Oct 10 2011 at 17:03:37 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2741 !!! WARNING: ASN 14 has a net charge of -0.2720 !!! WARNING: GLY 31 has a net charge of -0.2720 !!! WARNING: HIT 107 has a net charge of 0.5140 !!! WARNING: GLY 170 has a net charge of -0.2720 !!! WARNING: LEU 353 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.825746 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): 14.42800 71.12100 ymin,ymax (A): 3.787000 50.60200 zmin,zma (A): 6.807000 61.46400 x,y,z range (A): 56.69300 46.81500 54.65700 scale (grids/A): 2.825746 object centre (A): 42.77450 27.19450 34.13550 number of atom coordinates read : 2741 total number of charged atoms : 2602 net assigned charge : -3.573964 assigned positive charge : 410.9764 centred at (gu) : 85.64305 93.73118 96.85320 assigned negative charge : -414.5514 centred at (gu) : 85.26122 94.40654 97.25218 start vw surface at 0.1000000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 184406 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25187 grid for indexing accessible points = 1.400000 m= 89635 mr = 131724 m= 30680 mr = 72437 m= 6732 mr = 24146 m= 818 mr = 4941 m= 44 mr = 542 m= 0 mr = 10 time to grow re-entrant surface = 0.5599999 no. cavity mid-points inaccessible to solvent = 2935 time to turn everything in is 0.9800000 number of dielectric boundary points 78515 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.070000 number of grid points assigned charge 20816 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) : 1.883830 object centre at (A) : 42.77450 27.19450 34.13550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4197039 0.2273915 midg,1,midg; midg,igrid,midg 0.1536294 -0.3098040 1,midg,midg; igrid,midg,midg -0.6454128 0.3340214 gauss-seidel spectral radius is 0.9992747 estimated iterations to convergence 293 setup time was (sec) 1.220000 now iterating at: 17:03:39 rms-change max change #iterations 10.41438 409.9767 at 10iterations 6.183960 147.5214 at 20iterations 3.617215 81.61584 at 30iterations 2.123301 43.60365 at 40iterations 1.235866 25.57642 at 50iterations 0.7178811 14.59224 at 60iterations 0.4168301 8.834439 at 70iterations 0.2420220 4.696445 at 80iterations 0.1403658 2.710051 at 90iterations 8.1402309E-02 1.486540 at 100iterations 4.6912584E-02 0.7897758 at 110iterations 2.7120102E-02 0.4929056 at 120iterations 1.5685385E-02 0.2966461 at 130iterations 9.0551116E-03 0.1586113 at 140iterations 5.2357488E-03 0.1009998 at 150iterations 3.0252307E-03 6.6535950E-02 at 160iterations 1.7474822E-03 3.0776978E-02 at 170iterations 1.0115760E-03 1.9180298E-02 at 180iterations finished qdiffx linear iterations at : 17:03:50 total time elapsed so far: 12.55000 # loops : 180 mean,max change (kT/e) : 1.0115760E-03 1.9180298E-02 energy calculations done at 12.55000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.68000 DelPhi exited at 17:03:51 12.682u 0.198s 0:13.79 93.3% 0+0k 0+0io 0pf+0w