Mon Oct 10 19:20:51 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 Mon Oct 10 2011 at 19:20:52 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2948 !!! WARNING: GLU 548 has a net charge of -2.0000 !!! WARNING: GLU 564 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6124099 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): -22.21200 35.91900 ymin,ymax (A): -3.532000 49.44600 zmin,zma (A): -5.483000 48.30200 x,y,z range (A): 58.13100 52.97800 53.78500 scale (grids/A): 0.6124099 object centre (A): 6.853499 22.95700 21.40950 number of atom coordinates read : 2948 total number of charged atoms : 2806 net assigned charge : 1.3917685E-05 assigned positive charge : 440.3302 centred at (gu) : 88.76461 90.75629 92.69296 assigned negative charge : -440.3316 centred at (gu) : 88.76032 90.70779 92.67741 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 7588 nv = 96 ne = 84 npr = 56977 no. pairs analyzed = 56977 no. exposed pairs = 4166 no. arc points = 30459 no. surface atoms = 1400 nbur = 1548 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 396 mr = 3534 m= 5 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 4425 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3013 ## 283 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 9167 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.3638011E-10 1.6336006E-09 midg,1,midg; midg,igrid,midg -2.4950695E-09 3.3624106E-09 1,midg,midg; igrid,midg,midg -4.0502948E-10 1.5642862E-10 gauss-seidel spectral radius is 0.9862467 estimated iterations to convergence 70 setup time was (sec) 0.5400000 now iterating at: 19:20:52 rms-change max change #iterations 0.1248419 17.71634 at 10iterations 1.1080726E-02 1.521767 at 20iterations 9.8366698E-04 0.1259270 at 30iterations 8.8864406E-05 1.3237000E-02 at 40iterations 8.0093514E-06 1.0623932E-03 at 50iterations finished qdiffx linear iterations at : 19:20:55 total time elapsed so far: 2.960000 # loops : 50 mean,max change (kT/e) : 8.0093514E-06 1.0623932E-03 energy calculations done at 2.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.140000 DelPhi exited at 19:20:55 3.140u 0.151s 0:03.88 84.7% 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 19:20:55 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2948 !!! WARNING: GLU 548 has a net charge of -2.0000 !!! WARNING: GLU 564 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.837230 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): -22.21200 35.91900 ymin,ymax (A): -3.532000 49.44600 zmin,zma (A): -5.483000 48.30200 x,y,z range (A): 58.13100 52.97800 53.78500 scale (grids/A): 1.837230 object centre (A): 6.853499 22.95700 21.40950 number of atom coordinates read : 2948 total number of charged atoms : 2806 net assigned charge : 1.3917685E-05 assigned positive charge : 440.3302 centred at (gu) : 86.29317 92.26809 98.07803 assigned negative charge : -440.3316 centred at (gu) : 86.28069 92.12312 98.03188 start vw surface at 0.1600000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 80589 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30459 grid for indexing accessible points = 1.400000 m= 26510 mr = 50805 m= 4035 mr = 17756 m= 228 mr = 2178 m= 4 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 257 time to turn everything in is 0.5500000 number of dielectric boundary points 40587 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 219 iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 21950 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) : 0.6124099 object centre at (A) : 6.853499 22.95700 21.40950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.8107516E-04 -2.3274973E-02 midg,1,midg; midg,igrid,midg 1.6493794E-03 2.5777901E-02 1,midg,midg; igrid,midg,midg -2.5342194E-02 -3.7135072E-02 gauss-seidel spectral radius is 0.9986069 estimated iterations to convergence 212 setup time was (sec) 0.8100000 now iterating at: 19:20:56 rms-change max change #iterations 4.296964 172.6558 at 10iterations 1.969501 66.09626 at 20iterations 0.9140948 29.86361 at 30iterations 0.4251936 12.98820 at 40iterations 0.1961342 6.456105 at 50iterations 9.0915419E-02 2.936599 at 60iterations 4.2124517E-02 1.311303 at 70iterations 1.9549366E-02 0.7512636 at 80iterations 9.0912599E-03 0.2897970 at 90iterations 4.2211330E-03 0.1336036 at 100iterations 1.9547099E-03 6.4205170E-02 at 110iterations 9.1133441E-04 3.0376434E-02 at 120iterations finished qdiffx linear iterations at : 19:21:03 total time elapsed so far: 7.000000 # loops : 120 mean,max change (kT/e) : 9.1133441E-04 3.0376434E-02 energy calculations done at 7.000000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.170000 DelPhi exited at 19:21:03 7.169u 0.164s 0:07.61 96.1% 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 19:21:03 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2948 !!! WARNING: GLU 548 has a net charge of -2.0000 !!! WARNING: GLU 564 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.755845 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): -22.21200 35.91900 ymin,ymax (A): -3.532000 49.44600 zmin,zma (A): -5.483000 48.30200 x,y,z range (A): 58.13100 52.97800 53.78500 scale (grids/A): 2.755845 object centre (A): 6.853499 22.95700 21.40950 number of atom coordinates read : 2948 total number of charged atoms : 2806 net assigned charge : 1.3917685E-05 assigned positive charge : 440.3302 centred at (gu) : 84.43953 93.40180 102.1168 assigned negative charge : -440.3316 centred at (gu) : 84.42108 93.18475 102.0477 start vw surface at 0.1600000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 186396 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30459 grid for indexing accessible points = 1.400000 m= 85811 mr = 124896 m= 29961 mr = 65953 m= 7003 mr = 22321 m= 980 mr = 4878 m= 66 mr = 593 m= 1 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.8000000 no. cavity mid-points inaccessible to solvent = 772 time to turn everything in is 1.360000 number of dielectric boundary points 91565 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.490000 number of grid points assigned charge 22444 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) : 1.837230 object centre at (A) : 6.853499 22.95700 21.40950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.5026215E-03 -0.4735971 midg,1,midg; midg,igrid,midg -3.7014771E-02 0.2485390 1,midg,midg; igrid,midg,midg -0.1984743 -0.8052138 gauss-seidel spectral radius is 0.9992947 estimated iterations to convergence 297 setup time was (sec) 1.650000 now iterating at: 19:21:05 rms-change max change #iterations 10.44871 352.1015 at 10iterations 6.323023 136.0275 at 20iterations 3.776690 80.79124 at 30iterations 2.252674 45.79476 at 40iterations 1.333427 26.73913 at 50iterations 0.7873657 18.20515 at 60iterations 0.4639336 9.665726 at 70iterations 0.2720306 6.114841 at 80iterations 0.1597329 3.230647 at 90iterations 9.3552545E-02 1.849204 at 100iterations 5.4633733E-02 1.039116 at 110iterations 3.2008462E-02 0.6223221 at 120iterations 1.8662602E-02 0.3352737 at 130iterations 1.0901928E-02 0.2122192 at 140iterations 6.3606859E-03 0.1182899 at 150iterations 3.7103151E-03 6.8392754E-02 at 160iterations 2.1678167E-03 4.2284012E-02 at 170iterations 1.2628806E-03 2.1810532E-02 at 180iterations finished qdiffx linear iterations at : 19:21:14 total time elapsed so far: 11.20000 # loops : 180 mean,max change (kT/e) : 1.2628806E-03 2.1810532E-02 energy calculations done at 11.20000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.36000 DelPhi exited at 19:21:15 11.366u 0.165s 0:11.84 97.2% 0+0k 0+0io 0pf+0w