Sun Oct 9 12:34:29 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 12:34:29 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 = 2395 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6898823 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): -7.000000 44.26300 ymin,ymax (A): -13.99300 37.61000 zmin,zma (A): 1.705000 44.33700 x,y,z range (A): 51.26300 51.60300 42.63200 scale (grids/A): 0.6898823 object centre (A): 18.63150 11.80850 23.02100 number of atom coordinates read : 2395 total number of charged atoms : 2253 net assigned charge : 3.500024 assigned positive charge : 365.7010 centred at (gu) : 89.93703 91.12235 91.03114 assigned negative charge : -362.2016 centred at (gu) : 89.91535 91.30621 91.10148 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7742 nv = 96 ne = 84 npr = 47857 no. pairs analyzed = 47857 no. exposed pairs = 2946 no. arc points = 20384 no. surface atoms = 998 nbur = 1397 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 501 mr = 4429 m= 2 mr = 74 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 3742 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1888 ## 161 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 8681 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.8564259E-08 -8.4506997E-09 midg,1,midg; midg,igrid,midg 7.1638425E-08 -6.4882094E-08 1,midg,midg; igrid,midg,midg 1.2366263E-08 2.8481539E-08 gauss-seidel spectral radius is 0.9890853 estimated iterations to convergence 78 setup time was (sec) 0.4900000 now iterating at: 12:34:30 rms-change max change #iterations 0.1943527 34.05416 at 10iterations 2.3700049E-02 3.116743 at 20iterations 3.2493717E-03 0.4374123 at 30iterations 7.2478480E-04 9.5626831E-02 at 40iterations 2.4216766E-04 3.3115387E-02 at 50iterations finished qdiffx linear iterations at : 12:34:32 total time elapsed so far: 2.860000 # loops : 50 mean,max change (kT/e) : 2.4216766E-04 3.3115387E-02 energy calculations done at 2.860000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.060000 DelPhi exited at 12:34:32 3.059u 0.151s 0:03.50 91.4% 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 12:34:32 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 = 2395 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: 2.069647 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): -7.000000 44.26300 ymin,ymax (A): -13.99300 37.61000 zmin,zma (A): 1.705000 44.33700 x,y,z range (A): 51.26300 51.60300 42.63200 scale (grids/A): 2.069647 object centre (A): 18.63150 11.80850 23.02100 number of atom coordinates read : 2395 total number of charged atoms : 2253 net assigned charge : 3.500024 assigned positive charge : 365.7010 centred at (gu) : 89.81048 93.36668 93.09261 assigned negative charge : -362.2016 centred at (gu) : 89.74559 93.91834 93.30419 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 82369 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20384 grid for indexing accessible points = 1.400000 m= 32954 mr = 58176 m= 6017 mr = 24841 m= 566 mr = 3960 m= 12 mr = 313 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5700000 number of dielectric boundary points 34628 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 76 iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 17865 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) : 0.6898823 object centre at (A) : 18.63150 11.80850 23.02100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.1566526E-02 2.1982179E-03 midg,1,midg; midg,igrid,midg 1.8168850E-02 -6.8336785E-02 1,midg,midg; igrid,midg,midg 4.2613517E-02 3.8170258E-03 gauss-seidel spectral radius is 0.9988152 estimated iterations to convergence 230 setup time was (sec) 0.8300000 now iterating at: 12:34:33 rms-change max change #iterations 4.846402 261.8706 at 10iterations 2.380302 81.02953 at 20iterations 1.178060 33.92469 at 30iterations 0.5812250 19.16960 at 40iterations 0.2889608 8.920130 at 50iterations 0.1424240 4.218052 at 60iterations 7.0307493E-02 2.613098 at 70iterations 3.5010640E-02 1.036057 at 80iterations 1.7435314E-02 0.5226870 at 90iterations 8.7594250E-03 0.2433929 at 100iterations 4.5000403E-03 0.1216736 at 110iterations 2.3901726E-03 7.3345184E-02 at 120iterations finished qdiffx linear iterations at : 12:34:39 total time elapsed so far: 6.700000 # loops : 120 mean,max change (kT/e) : 2.3901726E-03 7.3345184E-02 energy calculations done at 6.700000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.870000 DelPhi exited at 12:34:40 6.874u 0.153s 0:07.32 95.9% 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 12:34:40 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 = 2395 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.104471 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): -7.000000 44.26300 ymin,ymax (A): -13.99300 37.61000 zmin,zma (A): 1.705000 44.33700 x,y,z range (A): 51.26300 51.60300 42.63200 scale (grids/A): 3.104471 object centre (A): 18.63150 11.80850 23.02100 number of atom coordinates read : 2395 total number of charged atoms : 2253 net assigned charge : 3.500024 assigned positive charge : 365.7010 centred at (gu) : 89.71561 95.04975 94.63885 assigned negative charge : -362.2016 centred at (gu) : 89.61842 95.87749 94.95627 start vw surface at 0.1500000 fill in re-entrant regions at 0.8100000 boundary points on vw surface= 189754 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20384 grid for indexing accessible points = 1.400000 m= 102759 mr = 139791 m= 41039 mr = 85391 m= 11412 mr = 33668 m= 2302 mr = 8811 m= 271 mr = 1697 m= 4 mr = 178 m= 0 mr = 2 time to grow re-entrant surface = 0.8900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.800000 number of dielectric boundary points 78003 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.930000 number of grid points assigned charge 18024 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) : 2.069647 object centre at (A) : 18.63150 11.80850 23.02100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5163820 -0.1112173 midg,1,midg; midg,igrid,midg 0.3577325 -0.7372203 1,midg,midg; igrid,midg,midg 0.4344800 -0.2435095 gauss-seidel spectral radius is 0.9992947 estimated iterations to convergence 297 setup time was (sec) 2.080000 now iterating at: 12:34:42 rms-change max change #iterations 10.87053 407.0174 at 10iterations 6.442087 143.2764 at 20iterations 3.815174 80.76333 at 30iterations 2.242611 40.04729 at 40iterations 1.322922 25.14711 at 50iterations 0.7757714 13.86631 at 60iterations 0.4563646 7.430237 at 70iterations 0.2674951 5.028831 at 80iterations 0.1570292 2.896183 at 90iterations 9.2047319E-02 1.774920 at 100iterations 5.3870302E-02 0.9661598 at 110iterations 3.1626947E-02 0.5304279 at 120iterations 1.8785184E-02 0.3101425 at 130iterations 1.1271203E-02 0.2158661 at 140iterations 6.9226329E-03 0.1295547 at 150iterations 4.4103009E-03 8.8764191E-02 at 160iterations 2.9725267E-03 6.3980103E-02 at 170iterations 2.1272297E-03 4.5164108E-02 at 180iterations finished qdiffx linear iterations at : 12:34:51 total time elapsed so far: 11.38000 # loops : 180 mean,max change (kT/e) : 2.1272297E-03 4.5164108E-02 energy calculations done at 11.38000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.55000 DelPhi exited at 12:34:52 11.557u 0.177s 0:12.00 97.6% 0+0k 0+0io 0pf+0w