Mon Oct 10 16:20:20 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 16:20:20 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: 345 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4811 !!! WARNING: GLM 131 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1600000 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 : 4811 total number of charged atoms : 4649 net assigned charge : 6.906020 assigned positive charge : 727.0906 centred at (gu) : 90.55700 89.95164 88.54876 assigned negative charge : -720.1891 centred at (gu) : 90.56145 89.98420 88.55362 start vw surface at 0.2300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 9334 nv = 96 ne = 84 npr = 98807 no. pairs analyzed = 98807 no. exposed pairs = 5833 no. arc points = 39165 no. surface atoms = 1957 nbur = 2854 mkacc time = 0.2300000 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= 374 mr = 5159 m= 1 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5100000 number of dielectric boundary points 4526 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4061 ## 496 charges are in solution ## iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 12384 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.8589796E-10 3.0833872E-10 midg,1,midg; midg,igrid,midg 9.0307362E-10 9.0337141E-11 1,midg,midg; igrid,midg,midg 4.7984489E-10 5.0083071E-10 gauss-seidel spectral radius is 0.9830620 estimated iterations to convergence 63 setup time was (sec) 0.7600000 now iterating at: 16:20:21 rms-change max change #iterations 9.9956848E-02 13.07880 at 10iterations 7.5204242E-03 0.9930992 at 20iterations 1.3794152E-03 0.2157745 at 30iterations 5.7369622E-04 7.7289581E-02 at 40iterations 2.6381735E-04 3.4013748E-02 at 50iterations finished qdiffx linear iterations at : 16:20:24 total time elapsed so far: 3.500000 # loops : 50 mean,max change (kT/e) : 2.6381735E-04 3.4013748E-02 energy calculations done at 3.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.690000 DelPhi exited at 16:20:24 3.696u 0.182s 0:04.16 93.0% 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 Mon Oct 10 2011 at 16:20:24 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: 345 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4811 !!! WARNING: GLM 131 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 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 : 4811 total number of charged atoms : 4649 net assigned charge : 6.906020 assigned positive charge : 727.0906 centred at (gu) : 91.66930 89.85341 85.64475 assigned negative charge : -720.1891 centred at (gu) : 91.68378 89.95232 85.66029 start vw surface at 0.2100000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 104313 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39165 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 33599 mr = 74250 m= 3721 mr = 23632 m= 103 mr = 1941 m= 0 mr = 16 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 1782 time to turn everything in is 0.7600000 number of dielectric boundary points 41897 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 453 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.8900000 number of grid points assigned charge 35697 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 1.4958895E-02 1.8560041E-02 midg,1,midg; midg,igrid,midg 1.3333481E-02 1.8900901E-02 1,midg,midg; igrid,midg,midg 4.8921383E-03 4.3966537E-03 gauss-seidel spectral radius is 0.9983942 estimated iterations to convergence 198 setup time was (sec) 1.070000 now iterating at: 16:20:26 rms-change max change #iterations 4.471687 160.9922 at 10iterations 1.965949 67.87177 at 20iterations 0.8639935 26.47415 at 30iterations 0.3802937 11.08055 at 40iterations 0.1673155 4.704983 at 50iterations 7.3794521E-02 2.132069 at 60iterations 3.2693017E-02 1.099102 at 70iterations 1.4587774E-02 0.4366989 at 80iterations 6.6722021E-03 0.2027588 at 90iterations 3.2592998E-03 9.8945618E-02 at 100iterations 1.7537342E-03 5.5547714E-02 at 110iterations 1.0877103E-03 3.0017853E-02 at 120iterations finished qdiffx linear iterations at : 16:20:33 total time elapsed so far: 8.170000 # loops : 120 mean,max change (kT/e) : 1.0877103E-03 3.0017853E-02 energy calculations done at 8.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.350000 DelPhi exited at 16:20:33 8.355u 0.217s 0:08.86 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 16:20:33 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: 345 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4811 !!! WARNING: GLM 131 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1600000 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 : 4811 total number of charged atoms : 4649 net assigned charge : 6.906020 assigned positive charge : 727.0906 centred at (gu) : 92.50360 89.77982 83.46665 assigned negative charge : -720.1891 centred at (gu) : 92.52557 89.92841 83.49027 start vw surface at 0.2400000 fill in re-entrant regions at 0.6500000 boundary points on vw surface= 242967 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39165 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 116001 mr = 181661 m= 33910 mr = 92929 m= 5838 mr = 25974 m= 487 mr = 3974 m= 11 mr = 261 m= 0 mr = 0 time to grow re-entrant surface = 1.100000 no. cavity mid-points inaccessible to solvent = 6004 time to turn everything in is 1.870000 number of dielectric boundary points 94415 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 16 iepsmp to db, and charging done at 2.010000 number of grid points assigned charge 37150 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 0.4488683 0.5604411 midg,1,midg; midg,igrid,midg 0.1354610 0.4357219 1,midg,midg; igrid,midg,midg 8.9841567E-02 9.3678728E-02 gauss-seidel spectral radius is 0.9992412 estimated iterations to convergence 287 setup time was (sec) 2.180000 now iterating at: 16:20:36 rms-change max change #iterations 11.58623 303.8911 at 10iterations 6.838606 162.2171 at 20iterations 4.009062 79.80647 at 30iterations 2.337304 47.42936 at 40iterations 1.355145 24.50941 at 50iterations 0.7849097 15.16840 at 60iterations 0.4538737 8.369656 at 70iterations 0.2620404 4.952023 at 80iterations 0.1509743 2.538507 at 90iterations 8.6868659E-02 1.483248 at 100iterations 4.9972124E-02 0.9303818 at 110iterations 2.8758997E-02 0.5166779 at 120iterations 1.6581357E-02 0.3243866 at 130iterations 9.6021667E-03 0.1575928 at 140iterations 5.6316666E-03 9.3811035E-02 at 150iterations 3.3719237E-03 5.4626465E-02 at 160iterations 2.0956891E-03 3.9102554E-02 at 170iterations 1.3826712E-03 2.4574280E-02 at 180iterations finished qdiffx linear iterations at : 16:20:46 total time elapsed so far: 12.51000 # loops : 180 mean,max change (kT/e) : 1.3826712E-03 2.4574280E-02 energy calculations done at 12.51000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.71000 DelPhi exited at 16:20:46 12.716u 0.172s 0:13.16 97.8% 0+0k 0+0io 0pf+0w