Mon Oct 10 18:52:08 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 18:52:08 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2120 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: 0.6290531 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): 0.6050001 40.41800 ymin,ymax (A): 37.48700 94.08000 zmin,zma (A): 16.11400 70.88300 x,y,z range (A): 39.81300 56.59300 54.76900 scale (grids/A): 0.6290531 object centre (A): 20.51150 65.78350 43.49850 number of atom coordinates read : 2120 total number of charged atoms : 1986 net assigned charge : 2.500004 assigned positive charge : 313.8044 centred at (gu) : 89.71950 87.56064 90.07443 assigned negative charge : -311.3049 centred at (gu) : 89.82955 87.66891 90.08880 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5806 nv = 96 ne = 84 npr = 42337 no. pairs analyzed = 42337 no. exposed pairs = 2727 no. arc points = 19356 no. surface atoms = 919 nbur = 1201 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 331 mr = 3189 m= 2 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 35 time to turn everything in is 0.3000000 number of dielectric boundary points 2908 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1911 ## 191 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 6928 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.3400631E-09 1.4416711E-09 midg,1,midg; midg,igrid,midg 1.6754171E-08 -2.9577769E-09 1,midg,midg; igrid,midg,midg 1.0498878E-08 -4.9176450E-09 gauss-seidel spectral radius is 0.9868735 estimated iterations to convergence 71 setup time was (sec) 0.5800000 now iterating at: 18:52:09 rms-change max change #iterations 0.1230479 22.17860 at 10iterations 1.1676232E-02 1.837482 at 20iterations 1.2746953E-03 0.2251663 at 30iterations 1.9908002E-04 3.5076141E-02 at 40iterations 4.5518715E-05 8.7337494E-03 at 50iterations finished qdiffx linear iterations at : 18:52:12 total time elapsed so far: 3.930000 # loops : 50 mean,max change (kT/e) : 4.5518715E-05 8.7337494E-03 energy calculations done at 3.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.110000 DelPhi exited at 18:52:13 4.110u 0.269s 0:04.84 90.2% 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 18:52:13 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2120 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: 1.887159 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): 0.6050001 40.41800 ymin,ymax (A): 37.48700 94.08000 zmin,zma (A): 16.11400 70.88300 x,y,z range (A): 39.81300 56.59300 54.76900 scale (grids/A): 1.887159 object centre (A): 20.51150 65.78350 43.49850 number of atom coordinates read : 2120 total number of charged atoms : 1986 net assigned charge : 2.500004 assigned positive charge : 313.8044 centred at (gu) : 89.15827 82.68153 90.22305 assigned negative charge : -311.3049 centred at (gu) : 89.48859 83.00670 90.26614 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 62701 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19356 grid for indexing accessible points = 1.400000 m= 22500 mr = 43288 m= 3598 mr = 16584 m= 218 mr = 2256 m= 2 mr = 88 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 651 time to turn everything in is 0.5700000 number of dielectric boundary points 26803 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 153 iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 15578 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) : 0.6290531 object centre at (A) : 20.51150 65.78350 43.49850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.2838417E-02 -1.0322677E-02 midg,1,midg; midg,igrid,midg 7.7774641E-03 6.5996950E-03 1,midg,midg; igrid,midg,midg 1.5533876E-02 -1.1479036E-03 gauss-seidel spectral radius is 0.9985648 estimated iterations to convergence 209 setup time was (sec) 0.8800000 now iterating at: 18:52:14 rms-change max change #iterations 3.708054 172.7440 at 10iterations 1.701774 68.77252 at 20iterations 0.7830002 29.39769 at 30iterations 0.3602222 14.24096 at 40iterations 0.1646371 5.901525 at 50iterations 7.5812750E-02 2.582907 at 60iterations 3.4922410E-02 1.333671 at 70iterations 1.6034314E-02 0.5865936 at 80iterations 7.3812306E-03 0.2546042 at 90iterations 3.4262983E-03 0.1111126 at 100iterations 1.5945461E-03 5.8953285E-02 at 110iterations 7.5182313E-04 2.7462006E-02 at 120iterations finished qdiffx linear iterations at : 18:52:23 total time elapsed so far: 9.270000 # loops : 120 mean,max change (kT/e) : 7.5182313E-04 2.7462006E-02 energy calculations done at 9.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.450000 DelPhi exited at 18:52:23 9.450u 0.309s 0:10.08 96.7% 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 Mon Oct 10 2011 at 18:52:23 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2120 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: 2.830739 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): 0.6050001 40.41800 ymin,ymax (A): 37.48700 94.08000 zmin,zma (A): 16.11400 70.88300 x,y,z range (A): 39.81300 56.59300 54.76900 scale (grids/A): 2.830739 object centre (A): 20.51150 65.78350 43.49850 number of atom coordinates read : 2120 total number of charged atoms : 1986 net assigned charge : 2.500004 assigned positive charge : 313.8044 centred at (gu) : 88.73743 79.02213 90.33443 assigned negative charge : -311.3049 centred at (gu) : 89.23284 79.51002 90.39923 start vw surface at 0.1500000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 144845 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19356 grid for indexing accessible points = 1.400000 m= 72770 mr = 104785 m= 26486 mr = 59669 m= 6380 mr = 21259 m= 938 mr = 4781 m= 60 mr = 625 m= 1 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.8600000 no. cavity mid-points inaccessible to solvent = 2172 time to turn everything in is 1.440000 number of dielectric boundary points 60333 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.590000 number of grid points assigned charge 15887 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) : 1.887159 object centre at (A) : 20.51150 65.78350 43.49850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4800951 -0.1884089 midg,1,midg; midg,igrid,midg 2.1809613E-02 0.2509139 1,midg,midg; igrid,midg,midg 0.1789108 1.3614397E-02 gauss-seidel spectral radius is 0.9992307 estimated iterations to convergence 285 setup time was (sec) 1.760000 now iterating at: 18:52:25 rms-change max change #iterations 8.779000 352.1413 at 10iterations 5.096980 122.4909 at 20iterations 2.930520 61.24653 at 30iterations 1.683835 39.51793 at 40iterations 0.9625045 19.53122 at 50iterations 0.5498328 11.78712 at 60iterations 0.3138063 6.753717 at 70iterations 0.1786646 3.728092 at 80iterations 0.1016779 2.039995 at 90iterations 5.7878349E-02 1.213863 at 100iterations 3.2897592E-02 0.7087498 at 110iterations 1.8728767E-02 0.3798066 at 120iterations 1.0673077E-02 0.2156715 at 130iterations 6.0739205E-03 0.1199684 at 140iterations 3.4753054E-03 7.1086884E-02 at 150iterations 1.9940294E-03 4.1908264E-02 at 160iterations 1.1560394E-03 2.3588181E-02 at 170iterations 6.7912770E-04 1.4482498E-02 at 180iterations finished qdiffx linear iterations at : 18:52:39 total time elapsed so far: 15.54000 # loops : 180 mean,max change (kT/e) : 6.7912770E-04 1.4482498E-02 energy calculations done at 15.54000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.72000 DelPhi exited at 18:52:40 15.720u 0.337s 0:16.57 96.8% 0+0k 0+0io 0pf+0w