Sat Oct 8 15:57:43 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 15:57:43 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 = 2305 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6413605 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): -17.85600 33.81100 ymin,ymax (A): 2.634000 47.90600 zmin,zma (A): -18.07500 37.43200 x,y,z range (A): 51.66700 45.27200 55.50700 scale (grids/A): 0.6413605 object centre (A): 7.977500 25.27000 9.678502 number of atom coordinates read : 2305 total number of charged atoms : 2245 net assigned charge : 5.000005 assigned positive charge : 344.8241 centred at (gu) : 88.68098 91.45579 89.99236 assigned negative charge : -339.8248 centred at (gu) : 88.62487 91.32288 90.01550 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 6408 nv = 96 ne = 84 npr = 45848 no. pairs analyzed = 45848 no. exposed pairs = 2973 no. arc points = 20316 no. surface atoms = 1012 nbur = 1293 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 322 mr = 3439 m= 0 mr = 61 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 21 time to turn everything in is 0.2800000 number of dielectric boundary points 3230 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2093 ## 205 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 7842 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.8605852E-09 4.9521121E-09 midg,1,midg; midg,igrid,midg -4.8915090E-09 2.9069730E-08 1,midg,midg; igrid,midg,midg 1.7733386E-09 1.0087741E-08 gauss-seidel spectral radius is 0.9873803 estimated iterations to convergence 73 setup time was (sec) 0.5300000 now iterating at: 15:57:44 rms-change max change #iterations 0.1352878 20.06901 at 10iterations 1.3712037E-02 2.055140 at 20iterations 1.5323092E-03 0.2230911 at 30iterations 2.7075503E-04 4.7733307E-02 at 40iterations 7.5719319E-05 1.3927460E-02 at 50iterations finished qdiffx linear iterations at : 15:57:48 total time elapsed so far: 4.180000 # loops : 50 mean,max change (kT/e) : 7.5719319E-05 1.3927460E-02 energy calculations done at 4.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.360000 DelPhi exited at 15:57:48 4.360u 0.400s 0:05.03 94.6% 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 Sat Oct 8 2011 at 15:57:48 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 = 2305 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.924082 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): -17.85600 33.81100 ymin,ymax (A): 2.634000 47.90600 zmin,zma (A): -18.07500 37.43200 x,y,z range (A): 51.66700 45.27200 55.50700 scale (grids/A): 1.924082 object centre (A): 7.977500 25.27000 9.678502 number of atom coordinates read : 2305 total number of charged atoms : 2245 net assigned charge : 5.000005 assigned positive charge : 344.8241 centred at (gu) : 86.04224 94.36697 89.97668 assigned negative charge : -339.8248 centred at (gu) : 85.87466 93.96850 90.04644 start vw surface at 0.1000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 69398 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20316 grid for indexing accessible points = 1.400000 m= 24521 mr = 47839 m= 4098 mr = 17813 m= 284 mr = 2636 m= 7 mr = 111 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 913 time to turn everything in is 0.5500000 number of dielectric boundary points 29909 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 129 iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 17686 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) : 0.6413605 object centre at (A) : 7.977500 25.27000 9.678502 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.6804446E-02 1.4452806E-02 midg,1,midg; midg,igrid,midg -5.5128201E-03 2.9145060E-02 1,midg,midg; igrid,midg,midg -4.7596905E-02 2.5026657E-02 gauss-seidel spectral radius is 0.9986331 estimated iterations to convergence 214 setup time was (sec) 0.8400000 now iterating at: 15:57:49 rms-change max change #iterations 4.044023 196.6029 at 10iterations 1.882129 69.04011 at 20iterations 0.8840785 31.82344 at 30iterations 0.4141639 14.12874 at 40iterations 0.1945297 6.297781 at 50iterations 9.1151915E-02 3.099930 at 60iterations 4.2683136E-02 1.468960 at 70iterations 2.0020504E-02 0.6266518 at 80iterations 9.4331019E-03 0.2902021 at 90iterations 4.4615432E-03 0.1428986 at 100iterations 2.1168015E-03 6.7037582E-02 at 110iterations 1.0229549E-03 3.4622669E-02 at 120iterations finished qdiffx linear iterations at : 15:57:59 total time elapsed so far: 10.24000 # loops : 120 mean,max change (kT/e) : 1.0229549E-03 3.4622669E-02 energy calculations done at 10.24000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.41000 DelPhi exited at 15:57:59 10.411u 0.500s 0:11.24 97.0% 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 15:57:59 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 = 2305 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.886122 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): -17.85600 33.81100 ymin,ymax (A): 2.634000 47.90600 zmin,zma (A): -18.07500 37.43200 x,y,z range (A): 51.66700 45.27200 55.50700 scale (grids/A): 2.886122 object centre (A): 7.977500 25.27000 9.678502 number of atom coordinates read : 2305 total number of charged atoms : 2245 net assigned charge : 5.000005 assigned positive charge : 344.8241 centred at (gu) : 84.06326 96.55027 89.96500 assigned negative charge : -339.8248 centred at (gu) : 83.81193 95.95274 90.06956 start vw surface at 0.1100000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 160650 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20316 grid for indexing accessible points = 1.400000 m= 79540 mr = 116335 m= 28718 mr = 64372 m= 7432 mr = 22955 m= 1137 mr = 5694 m= 78 mr = 786 m= 4 mr = 33 m= 0 mr = 0 time to grow re-entrant surface = 0.9000000 no. cavity mid-points inaccessible to solvent = 2791 time to turn everything in is 1.490000 number of dielectric boundary points 67384 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.630000 number of grid points assigned charge 17959 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) : 1.924082 object centre at (A) : 7.977500 25.27000 9.678502 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1855064 0.1485185 midg,1,midg; midg,igrid,midg -8.3104722E-02 0.2358692 1,midg,midg; igrid,midg,midg -0.7963278 0.4443157 gauss-seidel spectral radius is 0.9992571 estimated iterations to convergence 290 setup time was (sec) 1.830000 now iterating at: 15:58:02 rms-change max change #iterations 9.521548 361.7322 at 10iterations 5.592786 147.8000 at 20iterations 3.264858 64.34620 at 30iterations 1.906122 41.72126 at 40iterations 1.106138 24.40607 at 50iterations 0.6423019 15.01875 at 60iterations 0.3714272 7.371140 at 70iterations 0.2144091 3.996510 at 80iterations 0.1239939 2.380566 at 90iterations 7.1356401E-02 1.628278 at 100iterations 4.1129205E-02 0.7423601 at 110iterations 2.3777736E-02 0.4164914 at 120iterations 1.3681584E-02 0.2725410 at 130iterations 7.8717265E-03 0.1483569 at 140iterations 4.5313635E-03 8.2465172E-02 at 150iterations 2.6217799E-03 4.9240112E-02 at 160iterations 1.5195411E-03 2.8968811E-02 at 170iterations 8.9147879E-04 1.9224167E-02 at 180iterations finished qdiffx linear iterations at : 15:58:18 total time elapsed so far: 18.02000 # loops : 180 mean,max change (kT/e) : 8.9147879E-04 1.9224167E-02 energy calculations done at 18.02000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.18000 DelPhi exited at 15:58:18 18.181u 0.509s 0:18.96 98.5% 0+0k 0+0io 0pf+0w