Sat Oct 8 15:13:09 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 Sat Oct 8 2011 at 15:13:09 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3256 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: 0.6448107 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): 4.508000 59.11700 ymin,ymax (A): 2.927000 58.13700 zmin,zma (A): -61.16600 -9.298000 x,y,z range (A): 54.60900 55.21000 51.86800 scale (grids/A): 0.6448107 object centre (A): 31.81250 30.53200 -35.23200 number of atom coordinates read : 3256 total number of charged atoms : 3109 net assigned charge : 2.000011 assigned positive charge : 487.2617 centred at (gu) : 91.65765 90.86284 91.26330 assigned negative charge : -485.2632 centred at (gu) : 91.65830 90.81210 91.26951 start vw surface at 0.1800000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 9191 nv = 96 ne = 84 npr = 66936 no. pairs analyzed = 66936 no. exposed pairs = 3754 no. arc points = 25911 no. surface atoms = 1279 nbur = 1977 mkacc time = 0.2200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 460 mr = 5353 m= 4 mr = 53 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 28 time to turn everything in is 0.4800000 number of dielectric boundary points 4249 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2553 ## 231 charges are in solution ## iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 10997 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.3008916E-09 2.8734313E-09 midg,1,midg; midg,igrid,midg -4.2651069E-09 1.3951382E-08 1,midg,midg; igrid,midg,midg 2.4033451E-09 4.4330069E-09 gauss-seidel spectral radius is 0.9875944 estimated iterations to convergence 73 setup time was (sec) 0.8300000 now iterating at: 15:13:11 rms-change max change #iterations 0.1687697 23.00167 at 10iterations 1.7604765E-02 2.451659 at 20iterations 1.8445887E-03 0.2142258 at 30iterations 2.1580377E-04 2.7164459E-02 at 40iterations 3.8398004E-05 4.6653748E-03 at 50iterations finished qdiffx linear iterations at : 15:13:14 total time elapsed so far: 4.350000 # loops : 50 mean,max change (kT/e) : 3.8398004E-05 4.6653748E-03 energy calculations done at 4.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.570000 DelPhi exited at 15:13:15 4.572u 0.409s 0:05.31 93.5% 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 Sat Oct 8 2011 at 15:13:15 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3256 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: 1.934432 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): 4.508000 59.11700 ymin,ymax (A): 2.927000 58.13700 zmin,zma (A): -61.16600 -9.298000 x,y,z range (A): 54.60900 55.21000 51.86800 scale (grids/A): 1.934432 object centre (A): 31.81250 30.53200 -35.23200 number of atom coordinates read : 3256 total number of charged atoms : 3109 net assigned charge : 2.000011 assigned positive charge : 487.2617 centred at (gu) : 94.97214 92.58764 93.78884 assigned negative charge : -485.2632 centred at (gu) : 94.97474 92.43592 93.80819 start vw surface at 0.1800000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 99749 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25911 grid for indexing accessible points = 1.400000 m= 36736 mr = 71883 m= 5553 mr = 27684 m= 276 mr = 3543 m= 2 mr = 90 m= 0 mr = 0 time to grow re-entrant surface = 0.5200000 no. cavity mid-points inaccessible to solvent = 523 time to turn everything in is 0.9800000 number of dielectric boundary points 39116 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 160 iepsmp to db, and charging done at 1.110000 number of grid points assigned charge 24479 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) : 0.6448107 object centre at (A) : 31.81250 30.53200 -35.23200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.1119742E-03 1.7315102E-03 midg,1,midg; midg,igrid,midg -3.9558373E-02 -5.8650047E-02 1,midg,midg; igrid,midg,midg 2.6784267E-02 2.8139237E-02 gauss-seidel spectral radius is 0.9987327 estimated iterations to convergence 222 setup time was (sec) 1.310000 now iterating at: 15:13:16 rms-change max change #iterations 4.982699 180.1329 at 10iterations 2.406061 77.91898 at 20iterations 1.160244 31.24281 at 30iterations 0.5590016 16.77833 at 40iterations 0.2688909 7.754711 at 50iterations 0.1295718 3.825623 at 60iterations 6.2765464E-02 1.776451 at 70iterations 3.0160379E-02 0.8816605 at 80iterations 1.4559421E-02 0.4104939 at 90iterations 7.0181070E-03 0.2168579 at 100iterations 3.3882447E-03 8.8809967E-02 at 110iterations 1.6427707E-03 4.6892643E-02 at 120iterations finished qdiffx linear iterations at : 15:13:28 total time elapsed so far: 13.14000 # loops : 120 mean,max change (kT/e) : 1.6427707E-03 4.6892643E-02 energy calculations done at 13.14000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.35000 DelPhi exited at 15:13:29 13.354u 0.480s 0:14.08 98.2% 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 Sat Oct 8 2011 at 15:13:29 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3256 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: 2.901648 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): 4.508000 59.11700 ymin,ymax (A): 2.927000 58.13700 zmin,zma (A): -61.16600 -9.298000 x,y,z range (A): 54.60900 55.21000 51.86800 scale (grids/A): 2.901648 object centre (A): 31.81250 30.53200 -35.23200 number of atom coordinates read : 3256 total number of charged atoms : 3109 net assigned charge : 2.000011 assigned positive charge : 487.2617 centred at (gu) : 97.45809 93.88129 95.68316 assigned negative charge : -485.2632 centred at (gu) : 97.46208 93.65378 95.71220 start vw surface at 0.1600000 fill in re-entrant regions at 0.8800000 boundary points on vw surface= 230852 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25911 grid for indexing accessible points = 1.400000 m= 120217 mr = 173429 m= 42774 mr = 100260 m= 10050 mr = 34699 m= 1303 mr = 7717 m= 58 mr = 882 m= 0 mr = 21 time to grow re-entrant surface = 1.610000 no. cavity mid-points inaccessible to solvent = 1764 time to turn everything in is 2.680000 number of dielectric boundary points 88246 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 2.870000 number of grid points assigned charge 24871 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) : 1.934432 object centre at (A) : 31.81250 30.53200 -35.23200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.6526948E-02 -0.2367810 midg,1,midg; midg,igrid,midg -0.2614411 -0.8948715 1,midg,midg; igrid,midg,midg 0.3217119 0.1815383 gauss-seidel spectral radius is 0.9993002 estimated iterations to convergence 298 setup time was (sec) 3.080000 now iterating at: 15:13:32 rms-change max change #iterations 11.51900 379.1267 at 10iterations 6.812564 132.1624 at 20iterations 4.019899 68.05978 at 30iterations 2.368061 45.84821 at 40iterations 1.391635 23.45922 at 50iterations 0.8161559 13.21691 at 60iterations 0.4778579 7.659962 at 70iterations 0.2796447 4.605460 at 80iterations 0.1637940 2.665939 at 90iterations 9.5717885E-02 1.655701 at 100iterations 5.6061272E-02 0.9008329 at 110iterations 3.2819871E-02 0.5162864 at 120iterations 1.9168582E-02 0.3280602 at 130iterations 1.1255791E-02 0.1674805 at 140iterations 6.6195326E-03 0.1071310 at 150iterations 3.9016188E-03 5.6393385E-02 at 160iterations 2.3142006E-03 3.6895752E-02 at 170iterations 1.3909198E-03 2.6083946E-02 at 180iterations finished qdiffx linear iterations at : 15:13:49 total time elapsed so far: 19.75000 # loops : 180 mean,max change (kT/e) : 1.3909198E-03 2.6083946E-02 energy calculations done at 19.75000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.96000 DelPhi exited at 15:13:50 19.966u 0.486s 0:20.80 98.2% 0+0k 0+0io 0pf+0w