Sat Oct 8 18:07:00 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 8 2011 at 18:07:00 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 = 4693 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: 0.4983900 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): -33.03700 30.32000 ymin,ymax (A): -30.76000 30.84200 zmin,zma (A): 1.202000 72.63200 x,y,z range (A): 63.35700 61.60200 71.43000 scale (grids/A): 0.4983900 object centre (A): -1.358500 4.1000366E-02 36.91700 number of atom coordinates read : 4693 total number of charged atoms : 4538 net assigned charge : -9.999972 assigned positive charge : 713.6841 centred at (gu) : 89.03999 91.10659 89.60326 assigned negative charge : -723.6891 centred at (gu) : 89.00553 91.07186 89.56355 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 7598 nv = 96 ne = 84 npr = 91428 no. pairs analyzed = 91428 no. exposed pairs = 6244 no. arc points = 43729 no. surface atoms = 2081 nbur = 2612 mkacc time = 0.1600000 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 = 1.708000 m= 250 mr = 3756 m= 0 mr = 4 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 4088 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4208 ## 665 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 10076 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.5816239E-10 -1.8447197E-11 midg,1,midg; midg,igrid,midg -1.0031575E-10 -3.6242943E-11 1,midg,midg; igrid,midg,midg -1.7341438E-10 -2.2405539E-11 gauss-seidel spectral radius is 0.9794234 estimated iterations to convergence 58 setup time was (sec) 0.5100000 now iterating at: 18:07:00 rms-change max change #iterations 5.8148384E-02 12.83690 at 10iterations 3.2185055E-03 0.4804153 at 20iterations 3.4742735E-04 6.3050747E-02 at 30iterations 7.8258621E-05 1.5871048E-02 at 40iterations 1.9978863E-05 4.0545464E-03 at 50iterations finished qdiffx linear iterations at : 18:07:03 total time elapsed so far: 3.430000 # loops : 50 mean,max change (kT/e) : 1.9978863E-05 4.0545464E-03 energy calculations done at 3.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.570000 DelPhi exited at 18:07:04 3.570u 0.165s 0:04.07 91.6% 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 8 2011 at 18:07:04 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 = 4693 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: 1.495170 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): -33.03700 30.32000 ymin,ymax (A): -30.76000 30.84200 zmin,zma (A): 1.202000 72.63200 x,y,z range (A): 63.35700 61.60200 71.43000 scale (grids/A): 1.495170 object centre (A): -1.358500 4.1000366E-02 36.91700 number of atom coordinates read : 4693 total number of charged atoms : 4538 net assigned charge : -9.999972 assigned positive charge : 713.6841 centred at (gu) : 87.11842 93.31818 88.80803 assigned negative charge : -723.6891 centred at (gu) : 87.01645 93.21545 88.69041 start vw surface at 0.1200000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 84620 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43729 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 24198 mr = 55980 m= 1948 mr = 15826 m= 24 mr = 722 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 185 time to turn everything in is 0.4100000 number of dielectric boundary points 38262 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 584 ## 7 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 33769 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) : 0.4983900 object centre at (A) : -1.358500 4.1000366E-02 36.91700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.0438071E-02 1.0484872E-02 midg,1,midg; midg,igrid,midg -1.2821196E-02 -7.0681549E-03 1,midg,midg; igrid,midg,midg -3.2261389E-03 3.7367549E-03 gauss-seidel spectral radius is 0.9980014 estimated iterations to convergence 178 setup time was (sec) 0.6400000 now iterating at: 18:07:04 rms-change max change #iterations 3.578721 158.6862 at 10iterations 1.422741 53.55556 at 20iterations 0.5677564 20.91951 at 30iterations 0.2266588 7.990742 at 40iterations 9.0496033E-02 2.944777 at 50iterations 3.6280673E-02 1.345052 at 60iterations 1.4500549E-02 0.4990425 at 70iterations 5.8461805E-03 0.1955032 at 80iterations 2.3557553E-03 7.9216003E-02 at 90iterations 9.7164151E-04 3.6278725E-02 at 100iterations 4.1881297E-04 1.6238213E-02 at 110iterations 1.9186272E-04 7.5355768E-03 at 120iterations finished qdiffx linear iterations at : 18:07:12 total time elapsed so far: 7.880000 # loops : 120 mean,max change (kT/e) : 1.9186272E-04 7.5355768E-03 energy calculations done at 7.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.010000 DelPhi exited at 18:07:12 8.014u 0.206s 0:08.51 96.4% 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 Sat Oct 8 2011 at 18:07:12 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 = 4693 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: 2.242755 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): -33.03700 30.32000 ymin,ymax (A): -30.76000 30.84200 zmin,zma (A): 1.202000 72.63200 x,y,z range (A): 63.35700 61.60200 71.43000 scale (grids/A): 2.242755 object centre (A): -1.358500 4.1000366E-02 36.91700 number of atom coordinates read : 4693 total number of charged atoms : 4538 net assigned charge : -9.999972 assigned positive charge : 713.6841 centred at (gu) : 85.67732 94.97704 88.21182 assigned negative charge : -723.6891 centred at (gu) : 85.52444 94.82303 88.03569 start vw surface at 0.1200000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 196598 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43729 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 86666 mr = 137666 m= 21480 mr = 66630 m= 2558 mr = 15269 m= 100 mr = 1421 m= 1 mr = 29 m= 0 mr = 0 time to grow re-entrant surface = 0.5600001 no. cavity mid-points inaccessible to solvent = 706 time to turn everything in is 1.000000 number of dielectric boundary points 86388 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 87 iepsmp to db, and charging done at 1.100000 number of grid points assigned charge 36186 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) : 1.495170 object centre at (A) : -1.358500 4.1000366E-02 36.91700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3114182 0.2607234 midg,1,midg; midg,igrid,midg -0.3395109 -0.1207744 1,midg,midg; igrid,midg,midg -0.1175264 5.9527379E-02 gauss-seidel spectral radius is 0.9991227 estimated iterations to convergence 267 setup time was (sec) 1.240000 now iterating at: 18:07:14 rms-change max change #iterations 9.893213 293.7222 at 10iterations 5.627394 161.8210 at 20iterations 3.172473 85.76170 at 30iterations 1.774354 45.08810 at 40iterations 0.9878717 21.76571 at 50iterations 0.5484391 11.50539 at 60iterations 0.3038478 6.460263 at 70iterations 0.1674824 3.706786 at 80iterations 9.2545643E-02 2.289780 at 90iterations 5.0970048E-02 1.029963 at 100iterations 2.7972013E-02 0.5346723 at 110iterations 1.5366615E-02 0.2928054 at 120iterations 8.4434152E-03 0.1813593 at 130iterations 4.6204906E-03 9.3269348E-02 at 140iterations 2.5346484E-03 4.7677994E-02 at 150iterations 1.3930053E-03 2.5755882E-02 at 160iterations 7.6484034E-04 1.4909744E-02 at 170iterations 4.2034971E-04 8.0051422E-03 at 180iterations finished qdiffx linear iterations at : 18:07:25 total time elapsed so far: 13.08000 # loops : 180 mean,max change (kT/e) : 4.2034971E-04 8.0051422E-03 energy calculations done at 13.08000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.21000 DelPhi exited at 18:07:26 13.211u 0.210s 0:13.69 98.0% 0+0k 0+0io 0pf+0w