Wed Dec 28 11:01:40 PST 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 Wed Dec 28 2011 at 11:01:41 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: 277 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1965 !!! WARNING: ASH 25 has a net charge of -0.3190 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5876235 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): -35.22000 10.09900 ymin,ymax (A): 0.9390000 40.93000 zmin,zma (A): -2.192000 58.39100 x,y,z range (A): 45.31900 39.99100 60.58300 scale (grids/A): 0.5876235 object centre (A): -12.56050 20.93450 28.09950 number of atom coordinates read : 1965 total number of charged atoms : 1832 net assigned charge : 2.681006 assigned positive charge : 290.2140 centred at (gu) : 90.46455 89.71991 89.75471 assigned negative charge : -287.5332 centred at (gu) : 90.35857 89.85114 89.73395 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 4542 nv = 96 ne = 84 npr = 40416 no. pairs analyzed = 40416 no. exposed pairs = 2384 no. arc points = 17088 no. surface atoms = 804 nbur = 1161 mkacc time = 6.9999993E-02 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 = 1.456000 m= 191 mr = 2489 m= 0 mr = 15 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1700000 number of dielectric boundary points 2229 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1752 ## 224 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 5646 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.8667269E-10 1.0653262E-09 midg,1,midg; midg,igrid,midg 3.3207612E-09 -1.5795216E-09 1,midg,midg; igrid,midg,midg -1.0853116E-09 2.9659337E-09 gauss-seidel spectral radius is 0.9849644 estimated iterations to convergence 67 setup time was (sec) 0.4000000 now iterating at: 11:01:41 rms-change max change #iterations 8.3731882E-02 16.93500 at 10iterations 6.7684231E-03 1.335690 at 20iterations 5.3990231E-04 0.1164217 at 30iterations 4.3582357E-05 8.6669922E-03 at 40iterations 3.4462578E-06 6.3037872E-04 at 50iterations finished qdiffx linear iterations at : 11:01:45 total time elapsed so far: 4.110000 # loops : 50 mean,max change (kT/e) : 3.4462578E-06 6.3037872E-04 energy calculations done at 4.110000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.260000 DelPhi exited at 11:01:46 4.262u 0.346s 0:05.35 85.9% 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 Wed Dec 28 2011 at 11:01:46 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: 277 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1965 !!! WARNING: ASH 25 has a net charge of -0.3190 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.762871 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): -35.22000 10.09900 ymin,ymax (A): 0.9390000 40.93000 zmin,zma (A): -2.192000 58.39100 x,y,z range (A): 45.31900 39.99100 60.58300 scale (grids/A): 1.762871 object centre (A): -12.56050 20.93450 28.09950 number of atom coordinates read : 1965 total number of charged atoms : 1832 net assigned charge : 2.681006 assigned positive charge : 290.2140 centred at (gu) : 91.39379 89.15942 89.26385 assigned negative charge : -287.5332 centred at (gu) : 91.07584 89.55337 89.20187 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 49277 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17088 grid for indexing accessible points = 1.400000 m= 17099 mr = 33758 m= 2154 mr = 12882 m= 84 mr = 1304 m= 0 mr = 21 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 797 time to turn everything in is 0.3000000 number of dielectric boundary points 20649 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 214 iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 14283 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) : 0.5876235 object centre at (A) : -12.56050 20.93450 28.09950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.5532100E-02 2.1263016E-02 midg,1,midg; midg,igrid,midg 7.4881100E-04 -7.4103326E-03 1,midg,midg; igrid,midg,midg -3.0241278E-03 1.3204220E-03 gauss-seidel spectral radius is 0.9983298 estimated iterations to convergence 194 setup time was (sec) 0.6400000 now iterating at: 11:01:47 rms-change max change #iterations 3.093893 151.5215 at 10iterations 1.332815 62.73858 at 20iterations 0.5747964 22.14769 at 30iterations 0.2479988 9.775091 at 40iterations 0.1072648 4.294666 at 50iterations 4.6388619E-02 1.716108 at 60iterations 2.0021124E-02 0.7470322 at 70iterations 8.6244559E-03 0.3472061 at 80iterations 3.7190879E-03 0.1495152 at 90iterations 1.6134708E-03 6.1033726E-02 at 100iterations 6.9695362E-04 2.7484894E-02 at 110iterations 3.0170794E-04 1.3208389E-02 at 120iterations finished qdiffx linear iterations at : 11:01:57 total time elapsed so far: 10.05000 # loops : 120 mean,max change (kT/e) : 3.0170794E-04 1.3208389E-02 energy calculations done at 10.05000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.17000 DelPhi exited at 11:01:58 10.172u 0.458s 0:11.99 88.5% 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 Wed Dec 28 2011 at 11:01:58 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: 277 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1965 !!! WARNING: ASH 25 has a net charge of -0.3190 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.644306 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): -35.22000 10.09900 ymin,ymax (A): 0.9390000 40.93000 zmin,zma (A): -2.192000 58.39100 x,y,z range (A): 45.31900 39.99100 60.58300 scale (grids/A): 2.644306 object centre (A): -12.56050 20.93450 28.09950 number of atom coordinates read : 1965 total number of charged atoms : 1832 net assigned charge : 2.681006 assigned positive charge : 290.2140 centred at (gu) : 92.09070 88.73914 88.89577 assigned negative charge : -287.5332 centred at (gu) : 91.61372 89.33011 88.80282 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 113893 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17088 grid for indexing accessible points = 1.400000 m= 56847 mr = 81582 m= 19089 mr = 47116 m= 3591 mr = 15632 m= 325 mr = 2663 m= 6 mr = 223 m= 0 mr = 0 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 2666 time to turn everything in is 0.7600000 number of dielectric boundary points 46535 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 14651 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) : 1.762871 object centre at (A) : -12.56050 20.93450 28.09950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3127565 0.1555006 midg,1,midg; midg,igrid,midg -1.6928645E-02 -0.1043608 1,midg,midg; igrid,midg,midg -5.5394024E-02 -2.3050252E-02 gauss-seidel spectral radius is 0.9991496 estimated iterations to convergence 271 setup time was (sec) 1.080000 now iterating at: 11:02:00 rms-change max change #iterations 7.476452 257.3070 at 10iterations 4.143709 112.1312 at 20iterations 2.301134 56.74831 at 30iterations 1.269378 28.40421 at 40iterations 0.6973090 17.76463 at 50iterations 0.3837478 8.637875 at 60iterations 0.2111239 5.007591 at 70iterations 0.1159674 2.940802 at 80iterations 6.3837200E-02 1.535057 at 90iterations 3.5207704E-02 0.7573414 at 100iterations 1.9318489E-02 0.4377670 at 110iterations 1.0643130E-02 0.2644036 at 120iterations 5.8477535E-03 0.1297588 at 130iterations 3.2215454E-03 7.3040485E-02 at 140iterations 1.7731158E-03 3.9688110E-02 at 150iterations 9.7493705E-04 2.3069382E-02 at 160iterations 5.3796545E-04 1.1691093E-02 at 170iterations 2.9608759E-04 6.9923401E-03 at 180iterations finished qdiffx linear iterations at : 11:02:15 total time elapsed so far: 16.66000 # loops : 180 mean,max change (kT/e) : 2.9608759E-04 6.9923401E-03 energy calculations done at 16.66000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.79000 DelPhi exited at 11:02:18 16.793u 0.466s 0:19.61 87.9% 0+0k 0+0io 0pf+0w