Mon Oct 10 18:49:44 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 18:49:44 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 = 2585 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: 0.5747591 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): -14.10900 47.83000 ymin,ymax (A): 60.24600 115.6350 zmin,zma (A): 44.23400 87.93900 x,y,z range (A): 61.93900 55.38900 43.70501 scale (grids/A): 0.5747591 object centre (A): 16.86050 87.94050 66.08650 number of atom coordinates read : 2585 total number of charged atoms : 2486 net assigned charge : 1.000007 assigned positive charge : 399.6604 centred at (gu) : 87.71702 91.30687 91.05743 assigned negative charge : -398.6613 centred at (gu) : 87.81281 91.36395 91.19141 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 5659 nv = 96 ne = 84 npr = 50750 no. pairs analyzed = 50750 no. exposed pairs = 3262 no. arc points = 22438 no. surface atoms = 1082 nbur = 1503 mkacc time = 0.1100000 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 = 1.484000 m= 271 mr = 3096 m= 0 mr = 19 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 2815 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2317 ## 285 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 7264 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8240802E-09 -2.6532010E-09 midg,1,midg; midg,igrid,midg 8.1657114E-10 -1.0478549E-09 1,midg,midg; igrid,midg,midg 3.0191558E-09 -8.1626650E-10 gauss-seidel spectral radius is 0.9843442 estimated iterations to convergence 66 setup time was (sec) 0.4900000 now iterating at: 18:49:45 rms-change max change #iterations 8.7033130E-02 12.99526 at 10iterations 7.0868903E-03 1.276014 at 20iterations 7.4663409E-04 0.1262169 at 30iterations 1.5377857E-04 3.0482292E-02 at 40iterations 4.0877021E-05 8.2139969E-03 at 50iterations finished qdiffx linear iterations at : 18:49:47 total time elapsed so far: 2.910000 # loops : 50 mean,max change (kT/e) : 4.0877021E-05 8.2139969E-03 energy calculations done at 2.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.070000 DelPhi exited at 18:49:48 3.077u 0.159s 0:03.73 86.3% 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 Mon Oct 10 2011 at 18:49:48 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 = 2585 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: 1.724277 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): -14.10900 47.83000 ymin,ymax (A): 60.24600 115.6350 zmin,zma (A): 44.23400 87.93900 x,y,z range (A): 61.93900 55.38900 43.70501 scale (grids/A): 1.724277 object centre (A): 16.86050 87.94050 66.08650 number of atom coordinates read : 2585 total number of charged atoms : 2486 net assigned charge : 1.000007 assigned positive charge : 399.6604 centred at (gu) : 83.14992 93.91987 93.17156 assigned negative charge : -398.6613 centred at (gu) : 83.43813 94.09161 93.57381 start vw surface at 0.1600000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 62597 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22438 grid for indexing accessible points = 1.400000 m= 21455 mr = 43629 m= 2673 mr = 15567 m= 92 mr = 1512 m= 1 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 272 time to turn everything in is 0.4600000 number of dielectric boundary points 26092 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 229 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 19259 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) : 0.5747591 object centre at (A) : 16.86050 87.94050 66.08650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.0164481E-03 -7.1738404E-03 midg,1,midg; midg,igrid,midg 1.6432833E-02 -1.1064583E-02 1,midg,midg; igrid,midg,midg 1.7688766E-02 -1.1813623E-02 gauss-seidel spectral radius is 0.9983316 estimated iterations to convergence 194 setup time was (sec) 0.7100000 now iterating at: 18:49:49 rms-change max change #iterations 3.477514 216.9296 at 10iterations 1.499311 64.81207 at 20iterations 0.6472491 23.71300 at 30iterations 0.2810474 10.34855 at 40iterations 0.1209837 3.979750 at 50iterations 5.2510109E-02 1.895454 at 60iterations 2.2804813E-02 0.8871062 at 70iterations 9.8552443E-03 0.3999100 at 80iterations 4.3343017E-03 0.1641150 at 90iterations 1.9216350E-03 7.6402664E-02 at 100iterations 8.6738920E-04 3.0050278E-02 at 110iterations 4.0694664E-04 1.5668869E-02 at 120iterations finished qdiffx linear iterations at : 18:49:55 total time elapsed so far: 6.610000 # loops : 120 mean,max change (kT/e) : 4.0694664E-04 1.5668869E-02 energy calculations done at 6.610000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.780000 DelPhi exited at 18:49:56 6.785u 0.175s 0:07.45 93.2% 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 Mon Oct 10 2011 at 18:49:56 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 = 2585 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: 2.586416 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): -14.10900 47.83000 ymin,ymax (A): 60.24600 115.6350 zmin,zma (A): 44.23400 87.93900 x,y,z range (A): 61.93900 55.38900 43.70501 scale (grids/A): 2.586416 object centre (A): 16.86050 87.94050 66.08650 number of atom coordinates read : 2585 total number of charged atoms : 2486 net assigned charge : 1.000007 assigned positive charge : 399.6604 centred at (gu) : 79.72475 95.87986 94.75715 assigned negative charge : -398.6613 centred at (gu) : 80.15703 96.13744 95.36060 start vw surface at 0.1500000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 145301 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22438 grid for indexing accessible points = 1.400000 m= 71624 mr = 106324 m= 23622 mr = 58301 m= 4489 mr = 18616 m= 387 mr = 3179 m= 5 mr = 213 m= 0 mr = 2 time to grow re-entrant surface = 0.6000000 no. cavity mid-points inaccessible to solvent = 931 time to turn everything in is 1.060000 number of dielectric boundary points 58793 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 10 iepsmp to db, and charging done at 1.180000 number of grid points assigned charge 19874 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) : 1.724277 object centre at (A) : 16.86050 87.94050 66.08650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.1367489E-02 -6.9146737E-02 midg,1,midg; midg,igrid,midg 0.2862662 -0.1842098 1,midg,midg; igrid,midg,midg 0.5321239 2.7464696E-03 gauss-seidel spectral radius is 0.9991699 estimated iterations to convergence 274 setup time was (sec) 1.330000 now iterating at: 18:49:57 rms-change max change #iterations 8.854137 271.8709 at 10iterations 5.038016 153.8826 at 20iterations 2.856725 76.66566 at 30iterations 1.611935 41.72537 at 40iterations 0.9048719 19.65110 at 50iterations 0.5078262 13.57410 at 60iterations 0.2834912 5.954491 at 70iterations 0.1588214 3.392865 at 80iterations 8.8664420E-02 1.982233 at 90iterations 4.9528606E-02 1.020083 at 100iterations 2.7535940E-02 0.5823202 at 110iterations 1.5363490E-02 0.3336639 at 120iterations 8.5779978E-03 0.2009583 at 130iterations 4.7721942E-03 0.1105726 at 140iterations 2.6503957E-03 5.8498144E-02 at 150iterations 1.4881007E-03 3.1112671E-02 at 160iterations 8.3306903E-04 1.6494751E-02 at 170iterations 4.7048656E-04 9.3450546E-03 at 180iterations finished qdiffx linear iterations at : 18:50:06 total time elapsed so far: 10.54000 # loops : 180 mean,max change (kT/e) : 4.7048656E-04 9.3450546E-03 energy calculations done at 10.54000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.72000 DelPhi exited at 18:50:07 10.718u 0.188s 0:11.38 95.6% 0+0k 0+0io 0pf+0w