Tue Jan 24 23:01:33 PST 2012 #!/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 Tue Jan 24 2012 at 23:01:34 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 ! Automatically converted by prot2crg.py # of charge parameter records: 941 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4812 !!! WARNING: ZN1 901 has a net charge of 1.4000 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: 0.5496371 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): -63.08800 -7.559000 ymin,ymax (A): -34.81000 29.63000 zmin,zma (A): -29.13400 35.63600 x,y,z range (A): 55.52900 64.44000 64.77000 scale (grids/A): 0.5496371 object centre (A): -35.32350 -2.590001 3.251001 number of atom coordinates read : 4812 total number of charged atoms : 4654 net assigned charge : 8.400029 assigned positive charge : 725.6505 centred at (gu) : 90.53168 89.95081 88.54467 assigned negative charge : -717.2551 centred at (gu) : 90.53939 89.98655 88.54401 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 9355 nv = 96 ne = 84 npr = 98766 no. pairs analyzed = 98766 no. exposed pairs = 5813 no. arc points = 39039 no. surface atoms = 1950 nbur = 2862 mkacc time = 0.1700000 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 = 1.568000 m= 376 mr = 5193 m= 0 mr = 24 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 4514 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4058 ## 494 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 12390 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.4252427E-10 4.3209772E-10 midg,1,midg; midg,igrid,midg 1.0503098E-09 1.6018412E-10 1,midg,midg; igrid,midg,midg 6.1294214E-10 5.7528154E-10 gauss-seidel spectral radius is 0.9830620 estimated iterations to convergence 63 setup time was (sec) 0.5300000 now iterating at: 23:01:34 rms-change max change #iterations 9.7820066E-02 13.04489 at 10iterations 6.8672313E-03 0.8910990 at 20iterations 5.8711797E-04 7.9266906E-02 at 30iterations 1.3337322E-04 2.1028519E-02 at 40iterations 5.1486673E-05 6.8550110E-03 at 50iterations finished qdiffx linear iterations at : 23:01:37 total time elapsed so far: 3.430000 # loops : 50 mean,max change (kT/e) : 5.1486673E-05 6.8550110E-03 energy calculations done at 3.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.560000 DelPhi exited at 23:01:38 3.566u 0.174s 0:04.07 91.6% 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 Tue Jan 24 2012 at 23:01:38 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 ! Automatically converted by prot2crg.py # of charge parameter records: 941 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4812 !!! WARNING: ZN1 901 has a net charge of 1.4000 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: 1.648911 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): -63.08800 -7.559000 ymin,ymax (A): -34.81000 29.63000 zmin,zma (A): -29.13400 35.63600 x,y,z range (A): 55.52900 64.44000 64.77000 scale (grids/A): 1.648911 object centre (A): -35.32350 -2.590001 3.251001 number of atom coordinates read : 4812 total number of charged atoms : 4654 net assigned charge : 8.400029 assigned positive charge : 725.6505 centred at (gu) : 91.59341 89.85088 85.63243 assigned negative charge : -717.2551 centred at (gu) : 91.61767 89.95940 85.63148 start vw surface at 0.1500000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 104579 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39039 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 33756 mr = 74580 m= 3727 mr = 23792 m= 106 mr = 1954 m= 0 mr = 16 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 2443 time to turn everything in is 0.5200000 number of dielectric boundary points 41826 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 444 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 35736 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) : 0.5496371 object centre at (A) : -35.32350 -2.590001 3.251001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.6753033E-02 2.0047365E-02 midg,1,midg; midg,igrid,midg 1.5416749E-02 1.9750942E-02 1,midg,midg; igrid,midg,midg 5.9250351E-03 4.2764079E-03 gauss-seidel spectral radius is 0.9983940 estimated iterations to convergence 198 setup time was (sec) 0.7500000 now iterating at: 23:01:39 rms-change max change #iterations 4.449090 160.9827 at 10iterations 1.954891 68.10516 at 20iterations 0.8587906 26.46945 at 30iterations 0.3777357 11.27986 at 40iterations 0.1661959 4.777771 at 50iterations 7.3089302E-02 2.173809 at 60iterations 3.2251764E-02 0.8831768 at 70iterations 1.4210499E-02 0.4146700 at 80iterations 6.2610088E-03 0.1732845 at 90iterations 2.7886517E-03 7.7316284E-02 at 100iterations 1.2545956E-03 3.6591530E-02 at 110iterations 5.7841092E-04 1.8305779E-02 at 120iterations finished qdiffx linear iterations at : 23:01:46 total time elapsed so far: 8.070000 # loops : 120 mean,max change (kT/e) : 5.7841092E-04 1.8305779E-02 energy calculations done at 8.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.200000 DelPhi exited at 23:01:46 8.200u 0.215s 0:08.81 95.4% 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 Tue Jan 24 2012 at 23:01:46 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 ! Automatically converted by prot2crg.py # of charge parameter records: 941 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4812 !!! WARNING: ZN1 901 has a net charge of 1.4000 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: 2.473367 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): -63.08800 -7.559000 ymin,ymax (A): -34.81000 29.63000 zmin,zma (A): -29.13400 35.63600 x,y,z range (A): 55.52900 64.44000 64.77000 scale (grids/A): 2.473367 object centre (A): -35.32350 -2.590001 3.251001 number of atom coordinates read : 4812 total number of charged atoms : 4654 net assigned charge : 8.400029 assigned positive charge : 725.6505 centred at (gu) : 92.38976 89.77602 83.44817 assigned negative charge : -717.2551 centred at (gu) : 92.42644 89.93903 83.44707 start vw surface at 0.1300000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 243574 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39039 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 116605 mr = 182371 m= 34095 mr = 93603 m= 5829 mr = 26139 m= 491 mr = 3975 m= 11 mr = 261 m= 0 mr = 0 time to grow re-entrant surface = 0.7200000 no. cavity mid-points inaccessible to solvent = 8162 time to turn everything in is 1.250000 number of dielectric boundary points 94256 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 16 iepsmp to db, and charging done at 1.360000 number of grid points assigned charge 37190 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) : 1.648911 object centre at (A) : -35.32350 -2.590001 3.251001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4762535 0.5816634 midg,1,midg; midg,igrid,midg 0.1628122 0.4470766 1,midg,midg; igrid,midg,midg 0.1039457 7.9454921E-02 gauss-seidel spectral radius is 0.9992401 estimated iterations to convergence 286 setup time was (sec) 1.500000 now iterating at: 23:01:48 rms-change max change #iterations 11.53840 303.7770 at 10iterations 6.797185 170.4776 at 20iterations 3.981791 82.23294 at 30iterations 2.319923 49.20913 at 40iterations 1.343881 24.40267 at 50iterations 0.7777476 15.28407 at 60iterations 0.4494410 7.704602 at 70iterations 0.2589908 4.958776 at 80iterations 0.1492435 2.679764 at 90iterations 8.5745759E-02 1.549614 at 100iterations 4.9243625E-02 0.8389640 at 110iterations 2.8236033E-02 0.4947014 at 120iterations 1.6185399E-02 0.2665339 at 130iterations 9.2738690E-03 0.1570511 at 140iterations 5.3296345E-03 8.4026337E-02 at 150iterations 3.0676308E-03 4.7702789E-02 at 160iterations 1.7769031E-03 2.8611660E-02 at 170iterations 1.0432886E-03 1.8052101E-02 at 180iterations finished qdiffx linear iterations at : 23:02:00 total time elapsed so far: 13.43000 # loops : 180 mean,max change (kT/e) : 1.0432886E-03 1.8052101E-02 energy calculations done at 13.43000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.56000 DelPhi exited at 23:02:01 13.566u 0.238s 0:14.34 96.1% 0+0k 0+0io 0pf+0w