Tue Oct 11 03:19:58 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 Tue Oct 11 2011 at 03:19:58 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2705 !!! WARNING: HIR 128 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6089843 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): -27.46300 23.77000 ymin,ymax (A): 8.103000 66.56100 zmin,zma (A): -32.07700 25.27700 x,y,z range (A): 51.23300 58.45800 57.35400 scale (grids/A): 0.6089843 object centre (A): -1.846499 37.33200 -3.400000 number of atom coordinates read : 2705 total number of charged atoms : 2555 net assigned charge : -2.985989 assigned positive charge : 401.7307 centred at (gu) : 88.98878 87.58434 92.15598 assigned negative charge : -404.7177 centred at (gu) : 88.98377 87.54303 92.06854 start vw surface at 0.1700000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6882 nv = 96 ne = 84 npr = 52459 no. pairs analyzed = 52459 no. exposed pairs = 3828 no. arc points = 27498 no. surface atoms = 1262 nbur = 1443 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 317 mr = 3344 m= 0 mr = 23 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3832 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2710 ## 263 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 8411 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.7734331E-09 4.2616692E-09 midg,1,midg; midg,igrid,midg -6.5263857E-09 1.4800154E-10 1,midg,midg; igrid,midg,midg -2.4670428E-09 -1.1936290E-09 gauss-seidel spectral radius is 0.9860640 estimated iterations to convergence 69 setup time was (sec) 0.5800000 now iterating at: 03:19:59 rms-change max change #iterations 0.1188563 17.16253 at 10iterations 1.0235379E-02 1.725943 at 20iterations 9.1352244E-04 0.1303101 at 30iterations 8.0038568E-05 1.2466431E-02 at 40iterations 8.8066236E-06 1.3246536E-03 at 50iterations finished qdiffx linear iterations at : 03:20:01 total time elapsed so far: 3.410000 # loops : 50 mean,max change (kT/e) : 8.8066236E-06 1.3246536E-03 energy calculations done at 3.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.590000 DelPhi exited at 03:20:02 3.597u 0.220s 0:04.36 87.3% 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 03:20:02 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2705 !!! WARNING: HIR 128 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.826953 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): -27.46300 23.77000 ymin,ymax (A): 8.103000 66.56100 zmin,zma (A): -32.07700 25.27700 x,y,z range (A): 51.23300 58.45800 57.35400 scale (grids/A): 1.826953 object centre (A): -1.846499 37.33200 -3.400000 number of atom coordinates read : 2705 total number of charged atoms : 2555 net assigned charge : -2.985989 assigned positive charge : 401.7307 centred at (gu) : 86.96563 82.75231 96.46756 assigned negative charge : -404.7177 centred at (gu) : 86.95137 82.62888 96.20559 start vw surface at 0.2100000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 74279 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27498 grid for indexing accessible points = 1.400000 m= 24585 mr = 48255 m= 3035 mr = 16713 m= 135 mr = 1564 m= 2 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 295 time to turn everything in is 0.6200000 number of dielectric boundary points 35481 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 160 iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 20040 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) : 0.6089843 object centre at (A) : -1.846499 37.33200 -3.400000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.0700629E-02 3.6917612E-02 midg,1,midg; midg,igrid,midg -3.6627613E-02 -2.8035587E-02 1,midg,midg; igrid,midg,midg 2.2258277E-03 3.7367304E-03 gauss-seidel spectral radius is 0.9985462 estimated iterations to convergence 208 setup time was (sec) 0.9300000 now iterating at: 03:20:04 rms-change max change #iterations 4.027785 188.8159 at 10iterations 1.837079 68.97627 at 20iterations 0.8344877 28.61182 at 30iterations 0.3800104 11.61478 at 40iterations 0.1736071 6.235916 at 50iterations 7.8941524E-02 2.394348 at 60iterations 3.6079112E-02 1.311052 at 70iterations 1.6483713E-02 0.5921478 at 80iterations 7.5326324E-03 0.2646854 at 90iterations 3.4523362E-03 0.1108322 at 100iterations 1.5736492E-03 5.4041862E-02 at 110iterations 7.1786868E-04 2.3466110E-02 at 120iterations finished qdiffx linear iterations at : 03:20:11 total time elapsed so far: 8.100000 # loops : 120 mean,max change (kT/e) : 7.1786868E-04 2.3466110E-02 energy calculations done at 8.100000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.300000 DelPhi exited at 03:20:11 8.302u 0.210s 0:08.84 96.2% 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 Tue Oct 11 2011 at 03:20:11 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2705 !!! WARNING: HIR 128 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.740429 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): -27.46300 23.77000 ymin,ymax (A): 8.103000 66.56100 zmin,zma (A): -32.07700 25.27700 x,y,z range (A): 51.23300 58.45800 57.35400 scale (grids/A): 2.740429 object centre (A): -1.846499 37.33200 -3.400000 number of atom coordinates read : 2705 total number of charged atoms : 2555 net assigned charge : -2.985989 assigned positive charge : 401.7307 centred at (gu) : 85.44813 79.12833 99.70116 assigned negative charge : -404.7177 centred at (gu) : 85.42700 78.94324 99.30825 start vw surface at 0.1800000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 171685 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27498 grid for indexing accessible points = 1.400000 m= 81404 mr = 118060 m= 26198 mr = 63358 m= 5042 mr = 19623 m= 534 mr = 3332 m= 18 mr = 276 m= 0 mr = 2 time to grow re-entrant surface = 0.8099999 no. cavity mid-points inaccessible to solvent = 914 time to turn everything in is 1.440000 number of dielectric boundary points 80230 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.590000 number of grid points assigned charge 20436 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) : 1.826953 object centre at (A) : -1.846499 37.33200 -3.400000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.7461772 0.4219762 midg,1,midg; midg,igrid,midg -0.2152274 -0.5369730 1,midg,midg; igrid,midg,midg -8.8034905E-03 2.6207037E-02 gauss-seidel spectral radius is 0.9992613 estimated iterations to convergence 290 setup time was (sec) 1.780000 now iterating at: 03:20:13 rms-change max change #iterations 9.864717 289.5950 at 10iterations 5.848182 130.8195 at 20iterations 3.441020 83.31354 at 30iterations 2.014985 48.94909 at 40iterations 1.177040 26.64377 at 50iterations 0.6839197 13.71096 at 60iterations 0.3964344 8.742826 at 70iterations 0.2290807 4.934834 at 80iterations 0.1323611 2.547714 at 90iterations 7.6523595E-02 1.408928 at 100iterations 4.4096157E-02 0.8517151 at 110iterations 2.5450155E-02 0.5855751 at 120iterations 1.4641438E-02 0.2894406 at 130iterations 8.4129879E-03 0.2000580 at 140iterations 4.8537035E-03 9.3323708E-02 at 150iterations 2.7901577E-03 5.0544739E-02 at 160iterations 1.6091218E-03 2.8656006E-02 at 170iterations 9.2741899E-04 1.8820524E-02 at 180iterations finished qdiffx linear iterations at : 03:20:26 total time elapsed so far: 14.70000 # loops : 180 mean,max change (kT/e) : 9.2741899E-04 1.8820524E-02 energy calculations done at 14.70000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.89000 DelPhi exited at 03:20:27 14.893u 0.284s 0:15.67 96.8% 0+0k 0+0io 0pf+0w