Tue Oct 11 08:29:01 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 Tue Oct 11 2011 at 08:29:02 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2851 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 0.6514658 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): -12.18800 36.45500 ymin,ymax (A): -21.14400 27.26300 zmin,zma (A): -8.920000 45.72600 x,y,z range (A): 48.64300 48.40700 54.64600 scale (grids/A): 0.6514658 object centre (A): 12.13350 3.059501 18.40300 number of atom coordinates read : 2851 total number of charged atoms : 2697 net assigned charge : 1.140019 assigned positive charge : 430.1335 centred at (gu) : 90.23199 90.61000 91.21667 assigned negative charge : -428.9942 centred at (gu) : 89.97607 90.44598 91.10447 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 8080 nv = 96 ne = 84 npr = 59051 no. pairs analyzed = 59051 no. exposed pairs = 3335 no. arc points = 23361 no. surface atoms = 1128 nbur = 1723 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 469 mr = 4739 m= 1 mr = 56 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 30 time to turn everything in is 0.3500000 number of dielectric boundary points 3755 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2356 ## 244 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 9680 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.3913143E-08 2.7567104E-08 midg,1,midg; midg,igrid,midg -2.4044695E-08 3.4226819E-08 1,midg,midg; igrid,midg,midg -4.2092601E-08 4.7720427E-08 gauss-seidel spectral radius is 0.9878069 estimated iterations to convergence 74 setup time was (sec) 0.5900000 now iterating at: 08:29:02 rms-change max change #iterations 0.1657525 22.91481 at 10iterations 1.7323824E-02 2.182359 at 20iterations 1.8246234E-03 0.2379580 at 30iterations 2.0771960E-04 2.5112152E-02 at 40iterations 3.2347874E-05 4.0416718E-03 at 50iterations finished qdiffx linear iterations at : 08:29:05 total time elapsed so far: 3.230000 # loops : 50 mean,max change (kT/e) : 3.2347874E-05 4.0416718E-03 energy calculations done at 3.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.420000 DelPhi exited at 08:29:06 3.423u 0.137s 0:03.94 90.1% 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 Tue Oct 11 2011 at 08:29:06 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2851 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 1.954397 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): -12.18800 36.45500 ymin,ymax (A): -21.14400 27.26300 zmin,zma (A): -8.920000 45.72600 x,y,z range (A): 48.64300 48.40700 54.64600 scale (grids/A): 1.954397 object centre (A): 12.13350 3.059501 18.40300 number of atom coordinates read : 2851 total number of charged atoms : 2697 net assigned charge : 1.140019 assigned positive charge : 430.1335 centred at (gu) : 90.69554 91.82939 93.64960 assigned negative charge : -428.9942 centred at (gu) : 89.92796 91.33768 93.31285 start vw surface at 0.1600000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 87193 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23361 grid for indexing accessible points = 1.400000 m= 33205 mr = 62501 m= 5480 mr = 25269 m= 346 mr = 3618 m= 5 mr = 144 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 1591 time to turn everything in is 0.6500000 number of dielectric boundary points 34697 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 146 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 21274 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) : 0.6514658 object centre at (A) : 12.13350 3.059501 18.40300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.6898550E-02 -4.3962984E-03 midg,1,midg; midg,igrid,midg -1.6138984E-02 3.4578845E-02 1,midg,midg; igrid,midg,midg -1.7224023E-02 6.3668065E-02 gauss-seidel spectral radius is 0.9987199 estimated iterations to convergence 221 setup time was (sec) 0.9500000 now iterating at: 08:29:07 rms-change max change #iterations 4.718719 190.0371 at 10iterations 2.272247 70.19051 at 20iterations 1.094322 34.30022 at 30iterations 0.5267785 15.96857 at 40iterations 0.2522996 7.615015 at 50iterations 0.1217724 3.543608 at 60iterations 5.8620900E-02 1.683128 at 70iterations 2.8154062E-02 0.9465218 at 80iterations 1.3528948E-02 0.3669724 at 90iterations 6.5220748E-03 0.1785660 at 100iterations 3.1402092E-03 9.3987465E-02 at 110iterations 1.5172752E-03 4.1765213E-02 at 120iterations finished qdiffx linear iterations at : 08:29:14 total time elapsed so far: 7.820000 # loops : 120 mean,max change (kT/e) : 1.5172752E-03 4.1765213E-02 energy calculations done at 7.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.030000 DelPhi exited at 08:29:14 8.033u 0.218s 0:08.76 94.0% 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 Tue Oct 11 2011 at 08:29:14 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2851 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 2.931596 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): -12.18800 36.45500 ymin,ymax (A): -21.14400 27.26300 zmin,zma (A): -8.920000 45.72600 x,y,z range (A): 48.64300 48.40700 54.64600 scale (grids/A): 2.931596 object centre (A): 12.13350 3.059501 18.40300 number of atom coordinates read : 2851 total number of charged atoms : 2697 net assigned charge : 1.140019 assigned positive charge : 430.1335 centred at (gu) : 91.04314 92.74413 95.47404 assigned negative charge : -428.9942 centred at (gu) : 89.89194 92.00646 94.96924 start vw surface at 0.1700000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 201421 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23361 grid for indexing accessible points = 1.400000 m= 106499 mr = 150654 m= 40151 mr = 89135 m= 9973 mr = 33000 m= 1459 mr = 7703 m= 94 mr = 1003 m= 0 mr = 47 time to grow re-entrant surface = 1.020000 no. cavity mid-points inaccessible to solvent = 5272 time to turn everything in is 1.700000 number of dielectric boundary points 78055 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.850000 number of grid points assigned charge 21564 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) : 1.954397 object centre at (A) : 12.13350 3.059501 18.40300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.486515 0.1710791 midg,1,midg; midg,igrid,midg -0.2137777 0.3889737 1,midg,midg; igrid,midg,midg -0.1061960 0.5317144 gauss-seidel spectral radius is 0.9992794 estimated iterations to convergence 294 setup time was (sec) 2.020000 now iterating at: 08:29:17 rms-change max change #iterations 10.85648 454.1936 at 10iterations 6.359062 150.2615 at 20iterations 3.715449 79.05952 at 30iterations 2.174858 39.89452 at 40iterations 1.265531 23.04464 at 50iterations 0.7388282 12.87286 at 60iterations 0.4294044 7.339434 at 70iterations 0.2499530 5.014603 at 80iterations 0.1453024 2.659919 at 90iterations 8.4345445E-02 1.546033 at 100iterations 4.9037904E-02 0.8972130 at 110iterations 2.8408136E-02 0.4515705 at 120iterations 1.6504530E-02 0.2709284 at 130iterations 9.5827235E-03 0.1545897 at 140iterations 5.5777859E-03 8.9672089E-02 at 150iterations 3.2460536E-03 5.1978588E-02 at 160iterations 1.8966177E-03 3.0403137E-02 at 170iterations 1.1115938E-03 1.8280029E-02 at 180iterations finished qdiffx linear iterations at : 08:29:27 total time elapsed so far: 12.74000 # loops : 180 mean,max change (kT/e) : 1.1115938E-03 1.8280029E-02 energy calculations done at 12.74000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.92000 DelPhi exited at 08:29:28 12.923u 0.230s 0:13.49 97.4% 0+0k 0+0io 0pf+0w