Sun Oct 9 22:31:16 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 Sun Oct 9 2011 at 22:31:16 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: 264 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3038 !!! WARNING: SEP 141 has a net charge of -0.4750 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: 0.6704331 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): 45.63300 98.73300 ymin,ymax (A): 2.832000 54.66000 zmin,zma (A): 15.01000 67.72900 x,y,z range (A): 53.10000 51.82800 52.71900 scale (grids/A): 0.6704331 object centre (A): 72.18300 28.74600 41.36950 number of atom coordinates read : 3038 total number of charged atoms : 2988 net assigned charge : 2.025008 assigned positive charge : 474.8388 centred at (gu) : 90.54415 89.04276 90.58380 assigned negative charge : -472.8151 centred at (gu) : 90.37670 88.92551 90.61160 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 9599 nv = 96 ne = 84 npr = 56558 no. pairs analyzed = 56558 no. exposed pairs = 4246 no. arc points = 30669 no. surface atoms = 1407 nbur = 1631 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 604 mr = 4973 m= 3 mr = 77 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 7 time to turn everything in is 0.3200000 number of dielectric boundary points 5156 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2977 ## 268 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 11370 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3914576E-08 -2.0203796E-09 midg,1,midg; midg,igrid,midg -3.7039481E-08 3.5516123E-08 1,midg,midg; igrid,midg,midg -4.1360806E-08 6.5565281E-08 gauss-seidel spectral radius is 0.9885248 estimated iterations to convergence 76 setup time was (sec) 0.5400000 now iterating at: 22:31:16 rms-change max change #iterations 0.1956621 25.30025 at 10iterations 2.1620337E-02 2.878113 at 20iterations 2.4075091E-03 0.2970810 at 30iterations 2.7533367E-04 3.6298752E-02 at 40iterations 4.2486219E-05 5.0249100E-03 at 50iterations finished qdiffx linear iterations at : 22:31:19 total time elapsed so far: 2.940000 # loops : 50 mean,max change (kT/e) : 4.2486219E-05 5.0249100E-03 energy calculations done at 2.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.110000 DelPhi exited at 22:31:20 3.112u 0.156s 0:03.90 83.5% 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 Sun Oct 9 2011 at 22:31:20 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: 264 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3038 !!! WARNING: SEP 141 has a net charge of -0.4750 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: 2.011299 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): 45.63300 98.73300 ymin,ymax (A): 2.832000 54.66000 zmin,zma (A): 15.01000 67.72900 x,y,z range (A): 53.10000 51.82800 52.71900 scale (grids/A): 2.011299 object centre (A): 72.18300 28.74600 41.36950 number of atom coordinates read : 3038 total number of charged atoms : 2988 net assigned charge : 2.025008 assigned positive charge : 474.8388 centred at (gu) : 91.63168 87.12742 91.75081 assigned negative charge : -472.8151 centred at (gu) : 91.12975 86.77625 91.83463 start vw surface at 0.1500000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 102464 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30669 grid for indexing accessible points = 1.400000 m= 38247 mr = 68914 m= 7018 mr = 27435 m= 558 mr = 4346 m= 11 mr = 221 m= 0 mr = 0 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 1875 time to turn everything in is 0.6700000 number of dielectric boundary points 47382 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 168 iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 23655 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) : 0.6704331 object centre at (A) : 72.18300 28.74600 41.36950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.2263325E-03 -2.1139229E-02 midg,1,midg; midg,igrid,midg 2.6866019E-02 4.1617151E-02 1,midg,midg; igrid,midg,midg -6.7734295E-03 2.7211456E-02 gauss-seidel spectral radius is 0.9988348 estimated iterations to convergence 232 setup time was (sec) 0.9300000 now iterating at: 22:31:21 rms-change max change #iterations 5.269605 233.8505 at 10iterations 2.615346 75.79440 at 20iterations 1.290897 34.59837 at 30iterations 0.6389346 17.55814 at 40iterations 0.3160883 8.629151 at 50iterations 0.1567624 4.460320 at 60iterations 7.7418916E-02 2.355032 at 70iterations 3.8380764E-02 0.9931526 at 80iterations 1.8996391E-02 0.5604683 at 90iterations 9.4304364E-03 0.2655296 at 100iterations 4.6660150E-03 0.1313534 at 110iterations 2.3214705E-03 5.9198380E-02 at 120iterations finished qdiffx linear iterations at : 22:31:27 total time elapsed so far: 7.230000 # loops : 120 mean,max change (kT/e) : 2.3214705E-03 5.9198380E-02 energy calculations done at 7.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.430000 DelPhi exited at 22:31:28 7.428u 0.166s 0:07.86 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 Sun Oct 9 2011 at 22:31:28 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: 264 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3038 !!! WARNING: SEP 141 has a net charge of -0.4750 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: 3.016949 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): 45.63300 98.73300 ymin,ymax (A): 2.832000 54.66000 zmin,zma (A): 15.01000 67.72900 x,y,z range (A): 53.10000 51.82800 52.71900 scale (grids/A): 3.016949 object centre (A): 72.18300 28.74600 41.36950 number of atom coordinates read : 3038 total number of charged atoms : 2988 net assigned charge : 2.025008 assigned positive charge : 474.8388 centred at (gu) : 92.44731 85.69089 92.62594 assigned negative charge : -472.8151 centred at (gu) : 91.69463 85.16438 92.75179 start vw surface at 0.1500000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 236437 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30669 grid for indexing accessible points = 1.400000 m= 120835 mr = 167330 m= 46513 mr = 97083 m= 12724 mr = 36727 m= 2227 mr = 9380 m= 201 mr = 1504 m= 5 mr = 119 m= 0 mr = 0 time to grow re-entrant surface = 1.090000 no. cavity mid-points inaccessible to solvent = 6295 time to turn everything in is 1.760000 number of dielectric boundary points 106799 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.910000 number of grid points assigned charge 23904 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) : 2.011299 object centre at (A) : 72.18300 28.74600 41.36950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.0423751E-02 -0.3505026 midg,1,midg; midg,igrid,midg 0.1751290 0.2361614 1,midg,midg; igrid,midg,midg 0.1782533 0.3491787 gauss-seidel spectral radius is 0.9993433 estimated iterations to convergence 308 setup time was (sec) 2.060000 now iterating at: 22:31:30 rms-change max change #iterations 12.41160 424.5186 at 10iterations 7.604767 168.8811 at 20iterations 4.636245 99.80190 at 30iterations 2.813228 68.99489 at 40iterations 1.699998 36.72062 at 50iterations 1.022042 20.14972 at 60iterations 0.6154524 11.74518 at 70iterations 0.3678810 7.167039 at 80iterations 0.2205962 3.554428 at 90iterations 0.1318129 2.260714 at 100iterations 7.8559630E-02 1.226723 at 110iterations 4.6876583E-02 0.7291169 at 120iterations 2.7952414E-02 0.4495926 at 130iterations 1.6656365E-02 0.2667108 at 140iterations 9.9167330E-03 0.1576233 at 150iterations 5.9148674E-03 9.9114418E-02 at 160iterations 3.5153208E-03 5.6035995E-02 at 170iterations 2.0919403E-03 3.4320831E-02 at 180iterations finished qdiffx linear iterations at : 22:31:40 total time elapsed so far: 11.84000 # loops : 180 mean,max change (kT/e) : 2.0919403E-03 3.4320831E-02 energy calculations done at 11.84000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.01000 DelPhi exited at 22:31:40 12.017u 0.172s 0:12.46 97.7% 0+0k 0+0io 0pf+0w