Mon Oct 10 19:42:49 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 19:42:49 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: 245 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2591 !!! WARNING: HIR 118 has a net charge of 0.5140 !!! WARNING: HIR 244 has a net charge of 0.5140 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: 0.6587591 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): 6.348000 50.97000 ymin,ymax (A): -26.97600 23.81600 zmin,zma (A): -4.824000 49.21700 x,y,z range (A): 44.62200 50.79200 54.04100 scale (grids/A): 0.6587591 object centre (A): 28.65900 -1.580000 22.19650 number of atom coordinates read : 2591 total number of charged atoms : 2454 net assigned charge : 2.8008081E-02 assigned positive charge : 379.3080 centred at (gu) : 91.34947 91.18140 89.19928 assigned negative charge : -379.2809 centred at (gu) : 91.36784 91.13503 89.12991 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7653 nv = 96 ne = 84 npr = 52632 no. pairs analyzed = 52632 no. exposed pairs = 3520 no. arc points = 24093 no. surface atoms = 1182 nbur = 1409 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 491 mr = 4064 m= 5 mr = 65 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 4020 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2323 ## 187 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 8959 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.5321582E-08 1.0951435E-08 midg,1,midg; midg,igrid,midg -6.6733694E-09 1.1251410E-08 1,midg,midg; igrid,midg,midg 2.6699585E-09 -4.4187871E-09 gauss-seidel spectral radius is 0.9880641 estimated iterations to convergence 75 setup time was (sec) 0.5300000 now iterating at: 19:42:50 rms-change max change #iterations 0.1648914 25.32026 at 10iterations 1.7340682E-02 2.315308 at 20iterations 1.9310002E-03 0.2695618 at 30iterations 2.3827472E-04 3.4236908E-02 at 40iterations 4.4213022E-05 7.3509216E-03 at 50iterations finished qdiffx linear iterations at : 19:42:52 total time elapsed so far: 3.180000 # loops : 50 mean,max change (kT/e) : 4.4213022E-05 7.3509216E-03 energy calculations done at 3.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.350000 DelPhi exited at 19:42:53 3.358u 0.192s 0:03.86 91.7% 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 19:42:53 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: 245 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2591 !!! WARNING: HIR 118 has a net charge of 0.5140 !!! WARNING: HIR 244 has a net charge of 0.5140 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: 1.976277 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): 6.348000 50.97000 ymin,ymax (A): -26.97600 23.81600 zmin,zma (A): -4.824000 49.21700 x,y,z range (A): 44.62200 50.79200 54.04100 scale (grids/A): 1.976277 object centre (A): 28.65900 -1.580000 22.19650 number of atom coordinates read : 2591 total number of charged atoms : 2454 net assigned charge : 2.8008081E-02 assigned positive charge : 379.3080 centred at (gu) : 94.04784 93.54367 87.59739 assigned negative charge : -379.2809 centred at (gu) : 94.10336 93.40475 87.38966 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 81654 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24093 grid for indexing accessible points = 1.400000 m= 30277 mr = 55280 m= 5508 mr = 21850 m= 376 mr = 3370 m= 8 mr = 116 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6000000 number of dielectric boundary points 37207 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 100 iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 19407 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) : 0.6587591 object centre at (A) : 28.65900 -1.580000 22.19650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.4255540E-02 -1.8693857E-02 midg,1,midg; midg,igrid,midg 2.7179938E-02 1.3209299E-02 1,midg,midg; igrid,midg,midg 1.1076470E-02 -1.7424529E-02 gauss-seidel spectral radius is 0.9987404 estimated iterations to convergence 223 setup time was (sec) 0.9000000 now iterating at: 19:42:54 rms-change max change #iterations 4.522655 203.3295 at 10iterations 2.163557 68.38951 at 20iterations 1.044279 36.16742 at 30iterations 0.5020400 14.94031 at 40iterations 0.2429246 7.255710 at 50iterations 0.1165754 3.824753 at 60iterations 5.6275994E-02 1.621107 at 70iterations 2.7121818E-02 0.8137493 at 80iterations 1.3083439E-02 0.4184027 at 90iterations 6.3213017E-03 0.2301483 at 100iterations 3.0652066E-03 9.2610598E-02 at 110iterations 1.4762530E-03 4.3169022E-02 at 120iterations finished qdiffx linear iterations at : 19:43:01 total time elapsed so far: 7.610000 # loops : 120 mean,max change (kT/e) : 1.4762530E-03 4.3169022E-02 energy calculations done at 7.610000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.780000 DelPhi exited at 19:43:01 7.786u 0.221s 0:08.28 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 19:43:01 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: 245 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2591 !!! WARNING: HIR 118 has a net charge of 0.5140 !!! WARNING: HIR 244 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.964416 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): 6.348000 50.97000 ymin,ymax (A): -26.97600 23.81600 zmin,zma (A): -4.824000 49.21700 x,y,z range (A): 44.62200 50.79200 54.04100 scale (grids/A): 2.964416 object centre (A): 28.65900 -1.580000 22.19650 number of atom coordinates read : 2591 total number of charged atoms : 2454 net assigned charge : 2.8008081E-02 assigned positive charge : 379.3080 centred at (gu) : 96.07153 95.31535 86.39592 assigned negative charge : -379.2809 centred at (gu) : 96.15504 95.10717 86.08447 start vw surface at 0.1500000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 188884 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24093 grid for indexing accessible points = 1.400000 m= 95079 mr = 134764 m= 37524 mr = 76470 m= 9921 mr = 29705 m= 1544 mr = 7306 m= 107 mr = 959 m= 3 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 0.9299999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.560000 number of dielectric boundary points 83824 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.690000 number of grid points assigned charge 19632 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) : 1.976277 object centre at (A) : 28.65900 -1.580000 22.19650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2558761 -0.3619981 midg,1,midg; midg,igrid,midg 0.4347327 9.1591515E-02 1,midg,midg; igrid,midg,midg 0.1179908 -0.3220330 gauss-seidel spectral radius is 0.9992983 estimated iterations to convergence 298 setup time was (sec) 1.830000 now iterating at: 19:43:03 rms-change max change #iterations 10.69671 436.5547 at 10iterations 6.429193 166.7594 at 20iterations 3.841854 92.78005 at 30iterations 2.281114 53.51638 at 40iterations 1.350673 26.76458 at 50iterations 0.7987337 17.72534 at 60iterations 0.4692016 8.703237 at 70iterations 0.2760831 4.756912 at 80iterations 0.1623661 2.786873 at 90iterations 9.4863072E-02 1.749337 at 100iterations 5.5682234E-02 1.129715 at 110iterations 3.2625388E-02 0.5498762 at 120iterations 1.9118018E-02 0.3391781 at 130iterations 1.1176456E-02 0.1888275 at 140iterations 6.5760743E-03 0.1125908 at 150iterations 3.8670730E-03 6.5183640E-02 at 160iterations 2.2938454E-03 4.0002823E-02 at 170iterations 1.3737096E-03 2.2995949E-02 at 180iterations finished qdiffx linear iterations at : 19:43:13 total time elapsed so far: 11.54000 # loops : 180 mean,max change (kT/e) : 1.3737096E-03 2.2995949E-02 energy calculations done at 11.54000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.70000 DelPhi exited at 19:43:13 11.706u 0.201s 0:12.20 97.5% 0+0k 0+0io 0pf+0w