Wed Dec 28 11:02:07 PST 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 Wed Dec 28 2011 at 11:02:08 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: 277 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1967 !!! WARNING: ASH 25 has a net charge of -0.3190 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5867809 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): -35.16900 9.790999 ymin,ymax (A): 1.126000 41.17800 zmin,zma (A): -1.810000 58.86000 x,y,z range (A): 44.96000 40.05200 60.67000 scale (grids/A): 0.5867809 object centre (A): -12.68900 21.15200 28.52500 number of atom coordinates read : 1967 total number of charged atoms : 1834 net assigned charge : 0.6810054 assigned positive charge : 291.4540 centred at (gu) : 90.50234 89.59699 89.52449 assigned negative charge : -290.7733 centred at (gu) : 90.42151 89.71699 89.50536 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 4527 nv = 96 ne = 84 npr = 40417 no. pairs analyzed = 40417 no. exposed pairs = 2437 no. arc points = 16977 no. surface atoms = 828 nbur = 1139 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= 214 mr = 2476 m= 0 mr = 16 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 2249 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1759 ## 215 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 5582 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.9262349E-10 4.6335288E-10 midg,1,midg; midg,igrid,midg 2.5314040E-09 -1.8323050E-09 1,midg,midg; igrid,midg,midg -1.1489893E-09 1.8167081E-09 gauss-seidel spectral radius is 0.9849220 estimated iterations to convergence 67 setup time was (sec) 0.6300000 now iterating at: 11:02:09 rms-change max change #iterations 8.6468332E-02 19.19002 at 10iterations 6.8494738E-03 1.528107 at 20iterations 5.4258329E-04 0.1144037 at 30iterations 4.3147997E-05 7.1010590E-03 at 40iterations 3.4929610E-06 6.0462952E-04 at 50iterations finished qdiffx linear iterations at : 11:02:13 total time elapsed so far: 5.090000 # loops : 50 mean,max change (kT/e) : 3.4929610E-06 6.0462952E-04 energy calculations done at 5.090000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.290000 DelPhi exited at 11:02:15 5.295u 0.399s 0:07.99 71.0% 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 Wed Dec 28 2011 at 11:02:16 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: 277 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1967 !!! WARNING: ASH 25 has a net charge of -0.3190 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: 1.760343 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): -35.16900 9.790999 ymin,ymax (A): 1.126000 41.17800 zmin,zma (A): -1.810000 58.86000 x,y,z range (A): 44.96000 40.05200 60.67000 scale (grids/A): 1.760343 object centre (A): -12.68900 21.15200 28.52500 number of atom coordinates read : 1967 total number of charged atoms : 1834 net assigned charge : 0.6810054 assigned positive charge : 291.4540 centred at (gu) : 91.50699 88.79118 88.57352 assigned negative charge : -290.7733 centred at (gu) : 91.26471 89.15125 88.51643 start vw surface at 0.1400000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 48847 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16977 grid for indexing accessible points = 1.400000 m= 17206 mr = 33364 m= 2180 mr = 12965 m= 70 mr = 1282 m= 1 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4600000 number of dielectric boundary points 20675 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 180 iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 14271 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) : 0.5867809 object centre at (A) : -12.68900 21.15200 28.52500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.5490252E-02 2.0248761E-02 midg,1,midg; midg,igrid,midg -7.7534758E-04 -9.4637973E-03 1,midg,midg; igrid,midg,midg -4.5353808E-03 -4.9893921E-03 gauss-seidel spectral radius is 0.9983249 estimated iterations to convergence 194 setup time was (sec) 0.7600000 now iterating at: 11:02:17 rms-change max change #iterations 3.085867 179.7551 at 10iterations 1.327511 51.67262 at 20iterations 0.5740600 22.83391 at 30iterations 0.2482205 9.999844 at 40iterations 0.1067382 4.340019 at 50iterations 4.6052098E-02 1.945038 at 60iterations 1.9952614E-02 0.8404541 at 70iterations 8.5473573E-03 0.3360624 at 80iterations 3.6924351E-03 0.1489429 at 90iterations 1.6004558E-03 6.1955810E-02 at 100iterations 6.8986905E-04 2.7511597E-02 at 110iterations 2.9797744E-04 1.1793137E-02 at 120iterations finished qdiffx linear iterations at : 11:02:27 total time elapsed so far: 10.92000 # loops : 120 mean,max change (kT/e) : 2.9797744E-04 1.1793137E-02 energy calculations done at 10.92000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.12000 DelPhi exited at 11:02:28 11.124u 0.301s 0:11.92 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 Wed Dec 28 2011 at 11:02:28 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: 277 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1967 !!! WARNING: ASH 25 has a net charge of -0.3190 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.640514 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): -35.16900 9.790999 ymin,ymax (A): 1.126000 41.17800 zmin,zma (A): -1.810000 58.86000 x,y,z range (A): 44.96000 40.05200 60.67000 scale (grids/A): 2.640514 object centre (A): -12.68900 21.15200 28.52500 number of atom coordinates read : 1967 total number of charged atoms : 1834 net assigned charge : 0.6810054 assigned positive charge : 291.4540 centred at (gu) : 92.26051 88.18671 87.86032 assigned negative charge : -290.7733 centred at (gu) : 91.89722 88.72688 87.77466 start vw surface at 0.1400000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 113002 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16977 grid for indexing accessible points = 1.400000 m= 56686 mr = 80814 m= 19250 mr = 46864 m= 3615 mr = 15759 m= 355 mr = 2651 m= 8 mr = 235 m= 0 mr = 2 time to grow re-entrant surface = 0.6600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.160000 number of dielectric boundary points 46591 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.330000 number of grid points assigned charge 14665 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) : 1.760343 object centre at (A) : -12.68900 21.15200 28.52500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2819180 0.1725205 midg,1,midg; midg,igrid,midg -4.0072393E-02 -0.1373773 1,midg,midg; igrid,midg,midg -7.3333375E-02 -0.1113312 gauss-seidel spectral radius is 0.9991497 estimated iterations to convergence 271 setup time was (sec) 1.570000 now iterating at: 11:02:30 rms-change max change #iterations 7.463817 263.7452 at 10iterations 4.140915 131.6631 at 20iterations 2.294583 67.24467 at 30iterations 1.265290 32.63734 at 40iterations 0.6962507 17.03774 at 50iterations 0.3841003 8.920901 at 60iterations 0.2107059 4.846891 at 70iterations 0.1161829 3.225046 at 80iterations 6.4006291E-02 1.373077 at 90iterations 3.5256285E-02 0.8107882 at 100iterations 1.9345012E-02 0.5076475 at 110iterations 1.0695827E-02 0.2551727 at 120iterations 5.8648689E-03 0.1375027 at 130iterations 3.2233982E-03 7.0882797E-02 at 140iterations 1.7766656E-03 4.0853024E-02 at 150iterations 9.7690977E-04 2.2715494E-02 at 160iterations 5.3783366E-04 1.2503862E-02 at 170iterations 2.9653855E-04 6.5937042E-03 at 180iterations finished qdiffx linear iterations at : 11:02:47 total time elapsed so far: 18.64000 # loops : 180 mean,max change (kT/e) : 2.9653855E-04 6.5937042E-03 energy calculations done at 18.64000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.83000 DelPhi exited at 11:02:48 18.828u 0.582s 0:20.18 96.1% 0+0k 0+0io 0pf+0w