Sun Oct 9 15:36:34 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 Sun Oct 9 2011 at 15:36:34 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 # of charge parameter records: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5852 !!! WARNING: GLM 114 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5101456 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): 154.0140 222.8590 ymin,ymax (A): 90.86000 158.5390 zmin,zma (A): -2.145000 67.63900 x,y,z range (A): 68.84499 67.67900 69.78400 scale (grids/A): 0.5101456 object centre (A): 188.4365 124.6995 32.74700 number of atom coordinates read : 5852 total number of charged atoms : 5672 net assigned charge : -2.593963 assigned positive charge : 898.1596 centred at (gu) : 89.18531 89.34263 89.35641 assigned negative charge : -900.7618 centred at (gu) : 89.20398 89.40736 89.32598 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 9309 nv = 96 ne = 84 npr = 120843 no. pairs analyzed = 120843 no. exposed pairs = 6784 no. arc points = 46192 no. surface atoms = 2264 nbur = 3588 mkacc time = 0.2000000 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 = 1.652000 m= 285 mr = 5063 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 14 time to turn everything in is 0.3800000 number of dielectric boundary points 4524 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4503 ## 677 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 12589 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.6064725E-10 5.0091795E-11 midg,1,midg; midg,igrid,midg 2.0118485E-10 -2.0728191E-10 1,midg,midg; igrid,midg,midg 2.8168289E-11 -7.8678668E-11 gauss-seidel spectral radius is 0.9804091 estimated iterations to convergence 59 setup time was (sec) 0.5700000 now iterating at: 15:36:35 rms-change max change #iterations 7.5124905E-02 11.07229 at 10iterations 4.7407062E-03 0.6278381 at 20iterations 5.4702419E-04 7.4199677E-02 at 30iterations 1.1221554E-04 1.5005112E-02 at 40iterations 2.6225112E-05 3.3664703E-03 at 50iterations finished qdiffx linear iterations at : 15:36:38 total time elapsed so far: 3.500000 # loops : 50 mean,max change (kT/e) : 2.6225112E-05 3.3664703E-03 energy calculations done at 3.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.630000 DelPhi exited at 15:36:38 3.635u 0.184s 0:04.14 92.0% 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 Sun Oct 9 2011 at 15:36:38 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 # of charge parameter records: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5852 !!! WARNING: GLM 114 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.530437 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): 154.0140 222.8590 ymin,ymax (A): 90.86000 158.5390 zmin,zma (A): -2.145000 67.63900 x,y,z range (A): 68.84499 67.67900 69.78400 scale (grids/A): 1.530437 object centre (A): 188.4365 124.6995 32.74700 number of atom coordinates read : 5852 total number of charged atoms : 5672 net assigned charge : -2.593963 assigned positive charge : 898.1596 centred at (gu) : 87.55405 88.02624 88.06705 assigned negative charge : -900.7618 centred at (gu) : 87.61182 88.22198 87.97785 start vw surface at 0.1500000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 106446 reading accessible surface arcs data from file ARCDAT no. of arc points read = 46192 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 29948 mr = 75531 m= 2443 mr = 20364 m= 51 mr = 1059 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 1797 time to turn everything in is 0.5100000 number of dielectric boundary points 41934 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 641 ## 6 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 42473 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) : 0.5101456 object centre at (A) : 188.4365 124.6995 32.74700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.2181085E-03 -1.2141662E-02 midg,1,midg; midg,igrid,midg 1.1002925E-02 -8.7309629E-03 1,midg,midg; igrid,midg,midg -2.2368688E-02 2.0691880E-03 gauss-seidel spectral radius is 0.9981804 estimated iterations to convergence 186 setup time was (sec) 0.7500000 now iterating at: 15:36:39 rms-change max change #iterations 4.308378 159.7357 at 10iterations 1.795316 52.77324 at 20iterations 0.7470754 24.33565 at 30iterations 0.3125519 10.94937 at 40iterations 0.1307598 3.819305 at 50iterations 5.4605957E-02 1.583394 at 60iterations 2.2863543E-02 0.7770395 at 70iterations 9.6118022E-03 0.2988977 at 80iterations 4.0505319E-03 0.1206932 at 90iterations 1.7177941E-03 5.2143097E-02 at 100iterations 7.3337310E-04 2.2096634E-02 at 110iterations 3.2084587E-04 9.6397400E-03 at 120iterations finished qdiffx linear iterations at : 15:36:47 total time elapsed so far: 8.000000 # loops : 120 mean,max change (kT/e) : 3.2084587E-04 9.6397400E-03 energy calculations done at 8.000000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.130000 DelPhi exited at 15:36:47 8.134u 0.191s 0:08.59 96.8% 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 Sun Oct 9 2011 at 15:36:47 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5852 !!! WARNING: GLM 114 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.295655 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): 154.0140 222.8590 ymin,ymax (A): 90.86000 158.5390 zmin,zma (A): -2.145000 67.63900 x,y,z range (A): 68.84499 67.67900 69.78400 scale (grids/A): 2.295655 object centre (A): 188.4365 124.6995 32.74700 number of atom coordinates read : 5852 total number of charged atoms : 5672 net assigned charge : -2.593963 assigned positive charge : 898.1596 centred at (gu) : 86.33082 87.03912 87.10001 assigned negative charge : -900.7618 centred at (gu) : 86.41752 87.33283 86.96660 start vw surface at 0.1500000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 248852 reading accessible surface arcs data from file ARCDAT no. of arc points read = 46192 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 109399 mr = 185565 m= 26810 mr = 86750 m= 3485 mr = 19528 m= 147 mr = 2160 m= 1 mr = 29 m= 0 mr = 0 time to grow re-entrant surface = 0.6800001 no. cavity mid-points inaccessible to solvent = 5852 time to turn everything in is 1.240000 number of dielectric boundary points 94662 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 71 iepsmp to db, and charging done at 1.340000 number of grid points assigned charge 45262 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) : 1.530437 object centre at (A) : 188.4365 124.6995 32.74700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4734996 -0.2417074 midg,1,midg; midg,igrid,midg 0.2344225 -0.1428476 1,midg,midg; igrid,midg,midg -0.5742215 -5.4300842E-03 gauss-seidel spectral radius is 0.9991947 estimated iterations to convergence 278 setup time was (sec) 1.490000 now iterating at: 15:36:49 rms-change max change #iterations 11.51284 251.5612 at 10iterations 6.622247 142.4352 at 20iterations 3.790929 83.06786 at 30iterations 2.154585 45.50907 at 40iterations 1.222355 27.42096 at 50iterations 0.6909341 13.23112 at 60iterations 0.3897912 6.881443 at 70iterations 0.2199946 3.628952 at 80iterations 0.1241298 2.065837 at 90iterations 6.9655336E-02 1.192760 at 100iterations 3.9238796E-02 0.6627858 at 110iterations 2.2036292E-02 0.3793731 at 120iterations 1.2403497E-02 0.2177238 at 130iterations 6.9604875E-03 0.1201205 at 140iterations 3.9109206E-03 6.4224243E-02 at 150iterations 2.1997101E-03 4.0715218E-02 at 160iterations 1.2367102E-03 2.0233154E-02 at 170iterations 6.9541397E-04 1.1299133E-02 at 180iterations finished qdiffx linear iterations at : 15:37:01 total time elapsed so far: 13.41000 # loops : 180 mean,max change (kT/e) : 6.9541397E-04 1.1299133E-02 energy calculations done at 13.41000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.54000 DelPhi exited at 15:37:01 13.538u 0.218s 0:14.03 97.9% 0+0k 0+0io 0pf+0w