Sun Oct 9 20:07:57 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 Sun Oct 9 2011 at 20:07:57 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: 330 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5070 !!! WARNING: ASL 284 has a net charge of -0.1000 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: LLP 1 has a net charge of 1.7400 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 0.5461714 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): 3.265000 68.44600 ymin,ymax (A): -9.083000 53.50400 zmin,zma (A): -0.9860000 62.03300 x,y,z range (A): 65.18100 62.58700 63.01900 scale (grids/A): 0.5461714 object centre (A): 35.85550 22.21050 30.52350 number of atom coordinates read : 5070 total number of charged atoms : 4911 net assigned charge : 1.654048 assigned positive charge : 777.5844 centred at (gu) : 87.72677 89.32178 89.38403 assigned negative charge : -775.9358 centred at (gu) : 87.62547 89.34721 89.34868 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 10049 nv = 96 ne = 84 npr = 102044 no. pairs analyzed = 102044 no. exposed pairs = 5911 no. arc points = 40593 no. surface atoms = 2027 nbur = 3043 mkacc time = 0.2200000 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 = 1.568000 m= 416 mr = 5763 m= 2 mr = 33 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4600000 number of dielectric boundary points 4671 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4101 ## 464 charges are in solution ## iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 13090 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.2498554E-10 4.6492166E-10 midg,1,midg; midg,igrid,midg 5.0687265E-10 -1.3568796E-10 1,midg,midg; igrid,midg,midg -1.8906356E-09 7.3716011E-10 gauss-seidel spectral radius is 0.9828712 estimated iterations to convergence 63 setup time was (sec) 0.6700000 now iterating at: 20:07:58 rms-change max change #iterations 0.1054024 12.28333 at 10iterations 1.1677221E-02 1.576996 at 20iterations 4.3801833E-03 0.6732635 at 30iterations 2.0686665E-03 0.3248711 at 40iterations 9.8744116E-04 0.1561890 at 50iterations finished qdiffx linear iterations at : 20:08:00 total time elapsed so far: 3.110000 # loops : 50 mean,max change (kT/e) : 9.8744116E-04 0.1561890 energy calculations done at 3.110000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.290000 DelPhi exited at 20:08:01 3.290u 0.161s 0:03.73 92.4% 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 Sun Oct 9 2011 at 20:08:01 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: 330 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5070 !!! WARNING: ASL 284 has a net charge of -0.1000 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: LLP 1 has a net charge of 1.7400 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.638514 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): 3.265000 68.44600 ymin,ymax (A): -9.083000 53.50400 zmin,zma (A): -0.9860000 62.03300 x,y,z range (A): 65.18100 62.58700 63.01900 scale (grids/A): 1.638514 object centre (A): 35.85550 22.21050 30.52350 number of atom coordinates read : 5070 total number of charged atoms : 4911 net assigned charge : 1.654048 assigned positive charge : 777.5844 centred at (gu) : 83.17896 87.96402 88.15057 assigned negative charge : -775.9358 centred at (gu) : 82.87663 88.04141 88.04612 start vw surface at 0.1900000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 112447 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40593 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 38603 mr = 81710 m= 4510 mr = 28053 m= 137 mr = 2399 m= 0 mr = 14 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7700000 number of dielectric boundary points 43521 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 392 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.8900000 number of grid points assigned charge 37645 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) : 0.5461714 object centre at (A) : 35.85550 22.21050 30.52350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.6567422E-02 -1.4783110E-02 midg,1,midg; midg,igrid,midg 1.9856008E-02 1.0688132E-02 1,midg,midg; igrid,midg,midg -1.7742392E-02 1.7345699E-02 gauss-seidel spectral radius is 0.9983947 estimated iterations to convergence 198 setup time was (sec) 1.050000 now iterating at: 20:08:02 rms-change max change #iterations 4.715499 184.7686 at 10iterations 2.068149 61.07832 at 20iterations 0.9134277 27.71127 at 30iterations 0.4021613 10.70134 at 40iterations 0.1776409 5.475136 at 50iterations 7.9485938E-02 2.194558 at 60iterations 3.6357015E-02 0.9877625 at 70iterations 1.7737400E-02 0.5668240 at 80iterations 9.7395256E-03 0.3199463 at 90iterations 6.1450191E-03 0.1933365 at 100iterations 4.2821364E-03 0.1432724 at 110iterations 3.1592487E-03 9.7831726E-02 at 120iterations finished qdiffx linear iterations at : 20:08:08 total time elapsed so far: 7.250000 # loops : 120 mean,max change (kT/e) : 3.1592487E-03 9.7831726E-02 energy calculations done at 7.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.430000 DelPhi exited at 20:08:09 7.430u 0.194s 0:07.96 95.7% 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 Sun Oct 9 2011 at 20:08:09 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: 330 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5070 !!! WARNING: ASL 284 has a net charge of -0.1000 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: LLP 1 has a net charge of 1.7400 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.457772 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): 3.265000 68.44600 ymin,ymax (A): -9.083000 53.50400 zmin,zma (A): -0.9860000 62.03300 x,y,z range (A): 65.18100 62.58700 63.01900 scale (grids/A): 2.457772 object centre (A): 35.85550 22.21050 30.52350 number of atom coordinates read : 5070 total number of charged atoms : 4911 net assigned charge : 1.654048 assigned positive charge : 777.5844 centred at (gu) : 79.76823 86.94558 87.22566 assigned negative charge : -775.9358 centred at (gu) : 79.31489 87.06213 87.06924 start vw surface at 0.1900000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 261639 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40593 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 131791 mr = 199116 m= 40734 mr = 107878 m= 7322 mr = 31563 m= 582 mr = 4984 m= 14 mr = 298 m= 0 mr = 2 time to grow re-entrant surface = 1.150000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.850000 number of dielectric boundary points 98241 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 29 iepsmp to db, and charging done at 1.990000 number of grid points assigned charge 39232 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) : 1.638514 object centre at (A) : 35.85550 22.21050 30.52350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3568915 -0.3518616 midg,1,midg; midg,igrid,midg 0.1925203 3.0817820E-02 1,midg,midg; igrid,midg,midg -0.4298775 0.2659355 gauss-seidel spectral radius is 0.9992427 estimated iterations to convergence 287 setup time was (sec) 2.140000 now iterating at: 20:08:11 rms-change max change #iterations 11.94383 357.6949 at 10iterations 6.994519 137.2771 at 20iterations 4.065959 80.28821 at 30iterations 2.358843 48.17979 at 40iterations 1.361853 23.52978 at 50iterations 0.7857685 12.36667 at 60iterations 0.4529491 7.683714 at 70iterations 0.2602198 4.213223 at 80iterations 0.1497840 2.451468 at 90iterations 8.6355507E-02 1.339531 at 100iterations 4.9916171E-02 0.9267578 at 110iterations 2.9223062E-02 0.5304890 at 120iterations 1.7541710E-02 0.3310776 at 130iterations 1.0972210E-02 0.2121315 at 140iterations 7.2672493E-03 0.1477585 at 150iterations 5.1769712E-03 0.1066055 at 160iterations 3.9403625E-03 8.1348419E-02 at 170iterations 3.1433683E-03 6.2896729E-02 at 180iterations finished qdiffx linear iterations at : 20:08:21 total time elapsed so far: 11.79000 # loops : 180 mean,max change (kT/e) : 3.1433683E-03 6.2896729E-02 energy calculations done at 11.79000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.97000 DelPhi exited at 20:08:21 11.970u 0.202s 0:12.44 97.8% 0+0k 0+0io 0pf+0w