Tue Oct 11 00:27:41 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 Tue Oct 11 2011 at 00:27:41 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 = 4040 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: 0.4995159 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): 2.820000 65.68300 ymin,ymax (A): 7.930000 79.19901 zmin,zma (A): 17.46700 87.88600 x,y,z range (A): 62.86300 71.26900 70.41901 scale (grids/A): 0.4995159 object centre (A): 34.25150 43.56450 52.67650 number of atom coordinates read : 4040 total number of charged atoms : 3889 net assigned charge : 9.500041 assigned positive charge : 620.4280 centred at (gu) : 89.46204 90.44315 88.03365 assigned negative charge : -610.9308 centred at (gu) : 89.38530 90.60529 88.10033 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 6369 nv = 96 ne = 84 npr = 79224 no. pairs analyzed = 79224 no. exposed pairs = 5215 no. arc points = 36275 no. surface atoms = 1759 nbur = 2281 mkacc time = 0.1800000 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= 208 mr = 3123 m= 0 mr = 4 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 14 time to turn everything in is 0.4200000 number of dielectric boundary points 3450 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3558 ## 570 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 8598 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.9073582E-10 -5.1483999E-12 midg,1,midg; midg,igrid,midg 2.6322991E-10 -1.6369418E-10 1,midg,midg; igrid,midg,midg -2.9069138E-11 1.5951651E-10 gauss-seidel spectral radius is 0.9794593 estimated iterations to convergence 58 setup time was (sec) 0.6500000 now iterating at: 00:27:42 rms-change max change #iterations 5.5732459E-02 9.351885 at 10iterations 3.6143339E-03 0.7519455 at 20iterations 5.0827413E-04 0.1360321 at 30iterations 1.0087340E-04 2.8743744E-02 at 40iterations 2.0754829E-05 6.0081482E-03 at 50iterations finished qdiffx linear iterations at : 00:27:44 total time elapsed so far: 3.300000 # loops : 50 mean,max change (kT/e) : 2.0754829E-05 6.0081482E-03 energy calculations done at 3.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.500000 DelPhi exited at 00:27:45 3.499u 0.138s 0:04.14 87.4% 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 Oct 11 2011 at 00:27:45 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 = 4040 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: 1.498548 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): 2.820000 65.68300 ymin,ymax (A): 7.930000 79.19901 zmin,zma (A): 17.46700 87.88600 x,y,z range (A): 62.86300 71.26900 70.41901 scale (grids/A): 1.498548 object centre (A): 34.25150 43.56450 52.67650 number of atom coordinates read : 4040 total number of charged atoms : 3889 net assigned charge : 9.500041 assigned positive charge : 620.4280 centred at (gu) : 88.38488 91.32825 84.09966 assigned negative charge : -610.9308 centred at (gu) : 88.15589 91.81561 84.30054 start vw surface at 0.2000000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 71837 reading accessible surface arcs data from file ARCDAT no. of arc points read = 36275 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 19569 mr = 47416 m= 1483 mr = 12879 m= 22 mr = 607 m= 0 mr = 1 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 1497 time to turn everything in is 0.5700000 number of dielectric boundary points 32008 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 473 ## 8 charges are in solution ## iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 28949 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) : 0.4995159 object centre at (A) : 34.25150 43.56450 52.67650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.5013834E-03 -2.5525032E-02 midg,1,midg; midg,igrid,midg 2.8139543E-02 1.3429209E-02 1,midg,midg; igrid,midg,midg 3.1698816E-03 5.3808135E-03 gauss-seidel spectral radius is 0.9979258 estimated iterations to convergence 175 setup time was (sec) 0.8600000 now iterating at: 00:27:46 rms-change max change #iterations 3.259544 152.6956 at 10iterations 1.273939 49.68866 at 20iterations 0.4997279 18.60731 at 30iterations 0.1971531 7.054180 at 40iterations 7.7206545E-02 2.764458 at 50iterations 3.0407960E-02 1.236808 at 60iterations 1.2116659E-02 0.4121156 at 70iterations 4.8952485E-03 0.1861916 at 80iterations 2.0412272E-03 8.9675903E-02 at 90iterations 9.0265583E-04 4.3087006E-02 at 100iterations 4.2910010E-04 2.3086548E-02 at 110iterations 2.2332159E-04 1.2958527E-02 at 120iterations finished qdiffx linear iterations at : 00:27:53 total time elapsed so far: 7.480000 # loops : 120 mean,max change (kT/e) : 2.2332159E-04 1.2958527E-02 energy calculations done at 7.480000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.670000 DelPhi exited at 00:27:54 7.671u 0.228s 0:08.52 92.6% 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 Tue Oct 11 2011 at 00:27:54 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4040 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.247822 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): 2.820000 65.68300 ymin,ymax (A): 7.930000 79.19901 zmin,zma (A): 17.46700 87.88600 x,y,z range (A): 62.86300 71.26900 70.41901 scale (grids/A): 2.247822 object centre (A): 34.25150 43.56450 52.67650 number of atom coordinates read : 4040 total number of charged atoms : 3889 net assigned charge : 9.500041 assigned positive charge : 620.4280 centred at (gu) : 87.57689 91.99220 81.14923 assigned negative charge : -610.9308 centred at (gu) : 87.23382 92.72333 81.45084 start vw surface at 0.1800000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 167777 reading accessible surface arcs data from file ARCDAT no. of arc points read = 36275 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 71183 mr = 117564 m= 16995 mr = 54851 m= 2017 mr = 12242 m= 50 mr = 1155 m= 0 mr = 12 time to grow re-entrant surface = 0.7200000 no. cavity mid-points inaccessible to solvent = 4902 time to turn everything in is 1.280000 number of dielectric boundary points 72198 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 78 iepsmp to db, and charging done at 1.430000 number of grid points assigned charge 31005 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) : 1.498548 object centre at (A) : 34.25150 43.56450 52.67650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.9206594E-02 -0.4240005 midg,1,midg; midg,igrid,midg 0.4917010 0.2554360 1,midg,midg; igrid,midg,midg 0.1434827 0.1389446 gauss-seidel spectral radius is 0.9990742 estimated iterations to convergence 260 setup time was (sec) 1.600000 now iterating at: 00:27:56 rms-change max change #iterations 9.041560 290.2377 at 10iterations 5.007301 123.5054 at 20iterations 2.761879 75.02285 at 30iterations 1.507606 37.52877 at 40iterations 0.8220040 20.30294 at 50iterations 0.4468064 10.21083 at 60iterations 0.2417661 5.353928 at 70iterations 0.1307285 3.043592 at 80iterations 7.0501834E-02 1.732086 at 90iterations 3.8171716E-02 0.9549408 at 100iterations 2.0595562E-02 0.4566004 at 110iterations 1.1132349E-02 0.2499657 at 120iterations 6.0052318E-03 0.1277390 at 130iterations 3.2700307E-03 6.9472790E-02 at 140iterations 1.7809663E-03 3.9176941E-02 at 150iterations 9.7913307E-04 2.2785187E-02 at 160iterations 5.4718554E-04 1.4106750E-02 at 170iterations 3.1328970E-04 7.9193115E-03 at 180iterations finished qdiffx linear iterations at : 00:28:06 total time elapsed so far: 12.21000 # loops : 180 mean,max change (kT/e) : 3.1328970E-04 7.9193115E-03 energy calculations done at 12.21000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.40000 DelPhi exited at 00:28:07 12.402u 0.257s 0:13.12 96.4% 0+0k 0+0io 0pf+0w