Mon Oct 10 14:09:01 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 Mon Oct 10 2011 at 14:09:01 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 = 3934 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: 0.5579150 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): -50.27900 10.76300 ymin,ymax (A): -39.53900 24.27000 zmin,zma (A): -50.25900 1.823000 x,y,z range (A): 61.04200 63.80900 52.08200 scale (grids/A): 0.5579150 object centre (A): -19.75800 -7.634499 -24.21800 number of atom coordinates read : 3934 total number of charged atoms : 3789 net assigned charge : -2.499989 assigned positive charge : 605.8140 centred at (gu) : 88.59485 90.09831 90.71182 assigned negative charge : -608.3168 centred at (gu) : 88.63843 90.01740 90.67755 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 8028 nv = 96 ne = 84 npr = 78603 no. pairs analyzed = 78603 no. exposed pairs = 5056 no. arc points = 34931 no. surface atoms = 1694 nbur = 2240 mkacc time = 0.2300000 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 = 1.512000 m= 353 mr = 4249 m= 0 mr = 20 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4600000 number of dielectric boundary points 4112 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3548 ## 436 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 10524 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.2539052E-10 2.6453756E-10 midg,1,midg; midg,igrid,midg -1.3738914E-09 8.8699020E-10 1,midg,midg; igrid,midg,midg 5.0124066E-10 -6.2306155E-10 gauss-seidel spectral radius is 0.9835043 estimated iterations to convergence 64 setup time was (sec) 0.7300000 now iterating at: 14:09:02 rms-change max change #iterations 9.4937824E-02 13.39288 at 10iterations 6.8462230E-03 0.9310246 at 20iterations 5.2129000E-04 8.0600739E-02 at 30iterations 5.1256502E-05 6.6757202E-03 at 40iterations 1.0784471E-05 1.5211105E-03 at 50iterations finished qdiffx linear iterations at : 14:09:05 total time elapsed so far: 4.010000 # loops : 50 mean,max change (kT/e) : 1.0784471E-05 1.5211105E-03 energy calculations done at 4.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.190000 DelPhi exited at 14:09:06 4.193u 0.269s 0:05.02 88.6% 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 Mon Oct 10 2011 at 14:09:06 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 = 3934 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: 1.673745 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): -50.27900 10.76300 ymin,ymax (A): -39.53900 24.27000 zmin,zma (A): -50.25900 1.823000 x,y,z range (A): 61.04200 63.80900 52.08200 scale (grids/A): 1.673745 object centre (A): -19.75800 -7.634499 -24.21800 number of atom coordinates read : 3934 total number of charged atoms : 3789 net assigned charge : -2.499989 assigned positive charge : 605.8140 centred at (gu) : 85.78352 90.29377 92.13454 assigned negative charge : -608.3168 centred at (gu) : 85.91488 90.05155 92.03216 start vw surface at 0.1900000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 89699 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34931 grid for indexing accessible points = 1.400000 m= 28739 mr = 62509 m= 3284 mr = 19630 m= 96 mr = 1620 m= 1 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 1292 time to turn everything in is 0.7700000 number of dielectric boundary points 38048 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 367 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.9100000 number of grid points assigned charge 29152 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) : 0.5579150 object centre at (A) : -19.75800 -7.634499 -24.21800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.4439311E-03 -3.2143183E-03 midg,1,midg; midg,igrid,midg -2.1119727E-02 3.9173644E-03 1,midg,midg; igrid,midg,midg -3.8429413E-03 3.4854675E-03 gauss-seidel spectral radius is 0.9983764 estimated iterations to convergence 197 setup time was (sec) 1.070000 now iterating at: 14:09:07 rms-change max change #iterations 4.178099 158.0915 at 10iterations 1.823169 58.07729 at 20iterations 0.7976028 23.90895 at 30iterations 0.3483672 10.52047 at 40iterations 0.1526571 5.078434 at 50iterations 6.6770948E-02 2.038946 at 60iterations 2.9255945E-02 0.9074306 at 70iterations 1.2832779E-02 0.3851242 at 80iterations 5.6319451E-03 0.1727011 at 90iterations 2.4614471E-03 7.7064514E-02 at 100iterations 1.0817649E-03 3.6895752E-02 at 110iterations 4.7532970E-04 1.5159607E-02 at 120iterations finished qdiffx linear iterations at : 14:09:16 total time elapsed so far: 9.440000 # loops : 120 mean,max change (kT/e) : 4.7532970E-04 1.5159607E-02 energy calculations done at 9.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.620000 DelPhi exited at 14:09:16 9.622u 0.303s 0:10.35 95.8% 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 Mon Oct 10 2011 at 14:09:17 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 = 3934 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: 2.510618 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): -50.27900 10.76300 ymin,ymax (A): -39.53900 24.27000 zmin,zma (A): -50.25900 1.823000 x,y,z range (A): 61.04200 63.80900 52.08200 scale (grids/A): 2.510618 object centre (A): -19.75800 -7.634499 -24.21800 number of atom coordinates read : 3934 total number of charged atoms : 3789 net assigned charge : -2.499989 assigned positive charge : 605.8140 centred at (gu) : 83.67489 90.44035 93.20137 assigned negative charge : -608.3168 centred at (gu) : 83.87225 90.07730 93.04821 start vw surface at 0.2000000 fill in re-entrant regions at 0.6500000 boundary points on vw surface= 208573 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34931 grid for indexing accessible points = 1.400000 m= 98886 mr = 152838 m= 28991 mr = 78421 m= 5236 mr = 21296 m= 461 mr = 3458 m= 8 mr = 217 m= 0 mr = 0 time to grow re-entrant surface = 1.190000 no. cavity mid-points inaccessible to solvent = 4255 time to turn everything in is 1.970000 number of dielectric boundary points 85925 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 14 iepsmp to db, and charging done at 2.130000 number of grid points assigned charge 30275 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) : 1.673745 object centre at (A) : -19.75800 -7.634499 -24.21800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1009325 4.9881977E-03 midg,1,midg; midg,igrid,midg -0.3284099 -8.5493922E-03 1,midg,midg; igrid,midg,midg -0.2619491 7.2180681E-02 gauss-seidel spectral radius is 0.9992223 estimated iterations to convergence 283 setup time was (sec) 2.300000 now iterating at: 14:09:19 rms-change max change #iterations 10.83846 354.1797 at 10iterations 6.356276 153.6207 at 20iterations 3.693879 75.52533 at 30iterations 2.134914 42.86954 at 40iterations 1.233814 26.60320 at 50iterations 0.7073269 13.41774 at 60iterations 0.4055049 7.479943 at 70iterations 0.2319217 4.413628 at 80iterations 0.1325551 2.398245 at 90iterations 7.5307585E-02 1.380594 at 100iterations 4.2902008E-02 0.7335796 at 110iterations 2.4441121E-02 0.4408929 at 120iterations 1.3911122E-02 0.2363553 at 130iterations 7.9028653E-03 0.1318512 at 140iterations 4.4934321E-03 9.1419220E-02 at 150iterations 2.5515086E-03 4.6722889E-02 at 160iterations 1.4490990E-03 2.5877476E-02 at 170iterations 8.2237658E-04 1.4463425E-02 at 180iterations finished qdiffx linear iterations at : 14:09:33 total time elapsed so far: 16.25000 # loops : 180 mean,max change (kT/e) : 8.2237658E-04 1.4463425E-02 energy calculations done at 16.25000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.43000 DelPhi exited at 14:09:34 16.432u 0.284s 0:17.10 97.7% 0+0k 0+0io 0pf+0w