Mon Oct 10 09:44:31 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 09:44:31 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 = 2759 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: 0.6134757 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): -18.26500 33.75200 ymin,ymax (A): -59.21600 -1.186000 zmin,zma (A): -1.936000 52.74100 x,y,z range (A): 52.01700 58.03000 54.67700 scale (grids/A): 0.6134757 object centre (A): 7.743500 -30.20100 25.40250 number of atom coordinates read : 2759 total number of charged atoms : 2617 net assigned charge : 5.000013 assigned positive charge : 400.3501 centred at (gu) : 88.97467 87.98611 89.59418 assigned negative charge : -395.3504 centred at (gu) : 89.06459 87.82737 89.56987 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7128 nv = 96 ne = 84 npr = 53463 no. pairs analyzed = 53463 no. exposed pairs = 4241 no. arc points = 30355 no. surface atoms = 1404 nbur = 1355 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 405 mr = 3231 m= 2 mr = 19 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 4285 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2877 ## 249 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 8586 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.2600128E-09 4.3727995E-09 midg,1,midg; midg,igrid,midg -8.9423633E-09 7.7550633E-09 1,midg,midg; igrid,midg,midg 1.0532188E-08 -1.2511617E-09 gauss-seidel spectral radius is 0.9862753 estimated iterations to convergence 70 setup time was (sec) 0.4000000 now iterating at: 09:44:32 rms-change max change #iterations 0.1191540 18.90970 at 10iterations 1.0410835E-02 1.512793 at 20iterations 9.3814364E-04 0.1474236 at 30iterations 8.6456057E-05 1.3871193E-02 at 40iterations 8.8994557E-06 1.4357567E-03 at 50iterations finished qdiffx linear iterations at : 09:44:35 total time elapsed so far: 3.300000 # loops : 50 mean,max change (kT/e) : 8.8994557E-06 1.4357567E-03 energy calculations done at 3.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.440000 DelPhi exited at 09:44:35 3.441u 0.184s 0:03.93 92.1% 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 09:44:35 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 = 2759 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: 1.840427 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): -18.26500 33.75200 ymin,ymax (A): -59.21600 -1.186000 zmin,zma (A): -1.936000 52.74100 x,y,z range (A): 52.01700 58.03000 54.67700 scale (grids/A): 1.840427 object centre (A): 7.743500 -30.20100 25.40250 number of atom coordinates read : 2759 total number of charged atoms : 2617 net assigned charge : 5.000013 assigned positive charge : 400.3501 centred at (gu) : 86.92358 83.95760 88.78201 assigned negative charge : -395.3504 centred at (gu) : 87.19345 83.48178 88.70952 start vw surface at 0.1000000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 74993 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30355 grid for indexing accessible points = 1.400000 m= 25567 mr = 46174 m= 3852 mr = 16643 m= 197 mr = 1808 m= 3 mr = 38 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3900000 number of dielectric boundary points 39949 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 227 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 20533 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) : 0.6134757 object centre at (A) : 7.743500 -30.20100 25.40250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.1852582E-03 -1.2092987E-02 midg,1,midg; midg,igrid,midg 3.0848093E-02 4.4370003E-02 1,midg,midg; igrid,midg,midg 2.4921302E-02 1.3085645E-02 gauss-seidel spectral radius is 0.9985822 estimated iterations to convergence 211 setup time was (sec) 0.6100000 now iterating at: 09:44:36 rms-change max change #iterations 4.021130 193.9699 at 10iterations 1.847254 65.27011 at 20iterations 0.8484730 28.17248 at 30iterations 0.3920036 13.22428 at 40iterations 0.1802854 5.949190 at 50iterations 8.2793191E-02 2.755745 at 60iterations 3.8359407E-02 1.358788 at 70iterations 1.7639806E-02 0.5827999 at 80iterations 8.1367912E-03 0.2591352 at 90iterations 3.7412969E-03 0.1365509 at 100iterations 1.7289687E-03 6.0924530E-02 at 110iterations 7.9977489E-04 2.5762558E-02 at 120iterations finished qdiffx linear iterations at : 09:44:43 total time elapsed so far: 7.830000 # loops : 120 mean,max change (kT/e) : 7.9977489E-04 2.5762558E-02 energy calculations done at 7.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.970000 DelPhi exited at 09:44:44 7.972u 0.208s 0:08.45 96.6% 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 Mon Oct 10 2011 at 09:44:44 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 = 2759 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: 2.760641 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): -18.26500 33.75200 ymin,ymax (A): -59.21600 -1.186000 zmin,zma (A): -1.936000 52.74100 x,y,z range (A): 52.01700 58.03000 54.67700 scale (grids/A): 2.760641 object centre (A): 7.743500 -30.20100 25.40250 number of atom coordinates read : 2759 total number of charged atoms : 2617 net assigned charge : 5.000013 assigned positive charge : 400.3501 centred at (gu) : 85.38524 80.93626 88.17293 assigned negative charge : -395.3504 centred at (gu) : 85.79005 80.22270 88.06419 start vw surface at 0.1000000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 172839 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30355 grid for indexing accessible points = 1.400000 m= 81367 mr = 113745 m= 29037 mr = 61060 m= 6459 mr = 21286 m= 826 mr = 3956 m= 45 mr = 418 m= 0 mr = 12 time to grow re-entrant surface = 0.5500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9800000 number of dielectric boundary points 90096 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.070000 number of grid points assigned charge 20934 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) : 1.840427 object centre at (A) : 7.743500 -30.20100 25.40250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1754674 -0.1527706 midg,1,midg; midg,igrid,midg 0.4761609 0.5064771 1,midg,midg; igrid,midg,midg 0.2175502 0.1343802 gauss-seidel spectral radius is 0.9992779 estimated iterations to convergence 294 setup time was (sec) 1.210000 now iterating at: 09:44:45 rms-change max change #iterations 9.976194 519.0774 at 10iterations 6.021472 145.8372 at 20iterations 3.590271 88.07468 at 30iterations 2.119400 45.37551 at 40iterations 1.242527 30.66200 at 50iterations 0.7284999 14.65731 at 60iterations 0.4254601 9.465965 at 70iterations 0.2484024 5.486565 at 80iterations 0.1444505 3.445442 at 90iterations 8.4136449E-02 1.697012 at 100iterations 4.8945732E-02 1.001160 at 110iterations 2.8371973E-02 0.5918732 at 120iterations 1.6428690E-02 0.3375797 at 130iterations 9.5269931E-03 0.2220201 at 140iterations 5.5221389E-03 0.1269016 at 150iterations 3.2000048E-03 6.3394547E-02 at 160iterations 1.8542348E-03 3.9592743E-02 at 170iterations 1.0723457E-03 2.1086693E-02 at 180iterations finished qdiffx linear iterations at : 09:44:57 total time elapsed so far: 12.79000 # loops : 180 mean,max change (kT/e) : 1.0723457E-03 2.1086693E-02 energy calculations done at 12.79000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.91000 DelPhi exited at 09:44:57 12.916u 0.230s 0:13.53 97.1% 0+0k 0+0io 0pf+0w