Tue Nov 22 14:12:33 PST 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 Tue Nov 22 2011 at 14:12:39 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1958 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: 0.6085470 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): -34.78800 10.15900 ymin,ymax (A): 0.4570001 41.67900 zmin,zma (A): -1.696000 56.80400 x,y,z range (A): 44.94700 41.22200 58.50000 scale (grids/A): 0.6085470 object centre (A): -12.31450 21.06800 27.55400 number of atom coordinates read : 1958 total number of charged atoms : 1826 net assigned charge : 3.000004 assigned positive charge : 291.5539 centred at (gu) : 90.24747 89.59695 90.22974 assigned negative charge : -288.5542 centred at (gu) : 90.19215 89.73466 90.23580 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 4948 nv = 96 ne = 84 npr = 40192 no. pairs analyzed = 40192 no. exposed pairs = 2528 no. arc points = 17536 no. surface atoms = 858 nbur = 1100 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 233 mr = 2659 m= 1 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 6 time to turn everything in is 0.2400000 number of dielectric boundary points 2497 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1783 ## 200 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 5929 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.7906784E-09 1.5291191E-09 midg,1,midg; midg,igrid,midg 7.0617610E-09 -2.9682865E-09 1,midg,midg; igrid,midg,midg -2.7224173E-10 3.8112731E-09 gauss-seidel spectral radius is 0.9859664 estimated iterations to convergence 69 setup time was (sec) 0.4800000 now iterating at: 14:12:42 rms-change max change #iterations 0.1012457 20.63399 at 10iterations 8.8840025E-03 1.708235 at 20iterations 7.5428491E-04 0.1310921 at 30iterations 6.7774177E-05 1.3284206E-02 at 40iterations 5.8395894E-06 9.4604492E-04 at 50iterations finished qdiffx linear iterations at : 14:12:50 total time elapsed so far: 3.150000 # loops : 50 mean,max change (kT/e) : 5.8395894E-06 9.4604492E-04 energy calculations done at 3.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.330000 DelPhi exited at 14:12:52 3.337u 0.126s 0:14.48 23.8% 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 Tue Nov 22 2011 at 14:12:54 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1958 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: 1.825641 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): -34.78800 10.15900 ymin,ymax (A): 0.4570001 41.67900 zmin,zma (A): -1.696000 56.80400 x,y,z range (A): 44.94700 41.22200 58.50000 scale (grids/A): 1.825641 object centre (A): -12.31450 21.06800 27.55400 number of atom coordinates read : 1958 total number of charged atoms : 1826 net assigned charge : 3.000004 assigned positive charge : 291.5539 centred at (gu) : 90.74247 88.79039 90.68913 assigned negative charge : -288.5542 centred at (gu) : 90.57646 89.20412 90.70736 start vw surface at 0.1100000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 52894 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17536 grid for indexing accessible points = 1.400000 m= 19170 mr = 35993 m= 2870 mr = 14122 m= 152 mr = 1782 m= 1 mr = 62 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4200000 number of dielectric boundary points 23128 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 134 iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 14287 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) : 0.6085470 object centre at (A) : -12.31450 21.06800 27.55400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.6741145E-02 2.9206445E-02 midg,1,midg; midg,igrid,midg 3.7394920E-03 -6.5953904E-03 1,midg,midg; igrid,midg,midg -4.5301034E-03 -2.4131255E-03 gauss-seidel spectral radius is 0.9984401 estimated iterations to convergence 201 setup time was (sec) 0.7400000 now iterating at: 14:12:59 rms-change max change #iterations 3.343429 173.6761 at 10iterations 1.482900 63.11832 at 20iterations 0.6583808 24.99620 at 30iterations 0.2925814 11.37009 at 40iterations 0.1302701 4.561012 at 50iterations 5.7541154E-02 2.210433 at 60iterations 2.5689509E-02 0.9935308 at 70iterations 1.1347988E-02 0.4479430 at 80iterations 5.0121336E-03 0.1794739 at 90iterations 2.2423586E-03 8.1053734E-02 at 100iterations 9.9392910E-04 3.9298058E-02 at 110iterations 4.4236099E-04 1.6895294E-02 at 120iterations finished qdiffx linear iterations at : 14:13:22 total time elapsed so far: 8.320000 # loops : 120 mean,max change (kT/e) : 4.4236099E-04 1.6895294E-02 energy calculations done at 8.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.500000 DelPhi exited at 14:13:26 8.499u 0.247s 0:31.84 27.4% 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 Tue Nov 22 2011 at 14:13:28 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1958 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: 2.738461 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): -34.78800 10.15900 ymin,ymax (A): 0.4570001 41.67900 zmin,zma (A): -1.696000 56.80400 x,y,z range (A): 44.94700 41.22200 58.50000 scale (grids/A): 2.738461 object centre (A): -12.31450 21.06800 27.55400 number of atom coordinates read : 1958 total number of charged atoms : 1826 net assigned charge : 3.000004 assigned positive charge : 291.5539 centred at (gu) : 91.11366 88.18584 91.03365 assigned negative charge : -288.5542 centred at (gu) : 90.86483 88.80628 91.06110 start vw surface at 0.1200000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 122139 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17536 grid for indexing accessible points = 1.400000 m= 62106 mr = 87154 m= 22290 mr = 50787 m= 5067 mr = 17957 m= 639 mr = 3769 m= 32 mr = 428 m= 0 mr = 6 time to grow re-entrant surface = 0.6000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.040000 number of dielectric boundary points 52172 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.180000 number of grid points assigned charge 14605 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) : 1.825641 object centre at (A) : -12.31450 21.06800 27.55400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.3555560E-02 0.3269246 midg,1,midg; midg,igrid,midg -2.2068452E-02 -9.3946360E-02 1,midg,midg; igrid,midg,midg -8.1147209E-02 -6.9343589E-02 gauss-seidel spectral radius is 0.9991853 estimated iterations to convergence 277 setup time was (sec) 1.370000 now iterating at: 14:13:36 rms-change max change #iterations 8.137743 299.2033 at 10iterations 4.638598 112.9279 at 20iterations 2.634970 65.01990 at 30iterations 1.483738 39.19804 at 40iterations 0.8348527 21.10302 at 50iterations 0.4682077 10.18847 at 60iterations 0.2623413 5.635927 at 70iterations 0.1464222 2.980955 at 80iterations 8.1978142E-02 1.688936 at 90iterations 4.5779761E-02 1.097179 at 100iterations 2.5616935E-02 0.5597773 at 110iterations 1.4270766E-02 0.3194573 at 120iterations 7.9581644E-03 0.1592293 at 130iterations 4.4516637E-03 9.6686125E-02 at 140iterations 2.4793537E-03 5.3440094E-02 at 150iterations 1.3881860E-03 3.2262802E-02 at 160iterations 7.7355083E-04 1.6506195E-02 at 170iterations 4.3148902E-04 9.5963478E-03 at 180iterations finished qdiffx linear iterations at : 14:14:09 total time elapsed so far: 12.31000 # loops : 180 mean,max change (kT/e) : 4.3148902E-04 9.5963478E-03 energy calculations done at 12.31000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.50000 DelPhi exited at 14:14:12 12.500u 0.215s 0:44.54 28.5% 0+0k 0+0io 0pf+0w