Tue Oct 11 06:44:39 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 Tue Oct 11 2011 at 06:44:39 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2033 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 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= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6956929 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): -18.97500 23.83700 ymin,ymax (A): -12.31300 28.67300 zmin,zma (A): -3.136000 48.03600 x,y,z range (A): 42.81200 40.98600 51.17200 scale (grids/A): 0.6956929 object centre (A): 2.431000 8.180000 22.45000 number of atom coordinates read : 2033 total number of charged atoms : 1923 net assigned charge : 6.931010 assigned positive charge : 311.3571 centred at (gu) : 89.73310 89.76090 90.41906 assigned negative charge : -304.4261 centred at (gu) : 89.55339 89.78080 90.43011 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6730 nv = 96 ne = 84 npr = 40158 no. pairs analyzed = 40158 no. exposed pairs = 2479 no. arc points = 17159 no. surface atoms = 848 nbur = 1185 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 425 mr = 3828 m= 3 mr = 77 m= 0 mr = 0 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 3253 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1613 ## 157 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 7506 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.4713762E-08 4.3616694E-08 midg,1,midg; midg,igrid,midg 5.4147439E-08 3.5366647E-08 1,midg,midg; igrid,midg,midg -2.4739132E-08 1.0397366E-07 gauss-seidel spectral radius is 0.9892288 estimated iterations to convergence 78 setup time was (sec) 0.3600000 now iterating at: 06:44:39 rms-change max change #iterations 0.1854186 31.85340 at 10iterations 2.2242593E-02 3.034384 at 20iterations 3.0472784E-03 0.4663162 at 30iterations 5.4176769E-04 6.8313599E-02 at 40iterations 1.3726459E-04 1.5306473E-02 at 50iterations finished qdiffx linear iterations at : 06:44:42 total time elapsed so far: 3.170000 # loops : 50 mean,max change (kT/e) : 1.3726459E-04 1.5306473E-02 energy calculations done at 3.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.300000 DelPhi exited at 06:44:42 3.308u 0.156s 0:03.77 91.5% 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 Tue Oct 11 2011 at 06:44:42 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2033 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 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= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.087079 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): -18.97500 23.83700 ymin,ymax (A): -12.31300 28.67300 zmin,zma (A): -3.136000 48.03600 x,y,z range (A): 42.81200 40.98600 51.17200 scale (grids/A): 2.087079 object centre (A): 2.431000 8.180000 22.45000 number of atom coordinates read : 2033 total number of charged atoms : 1923 net assigned charge : 6.931010 assigned positive charge : 311.3571 centred at (gu) : 89.19940 89.28278 91.25714 assigned negative charge : -304.4261 centred at (gu) : 88.66032 89.34238 91.29066 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 71448 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17159 grid for indexing accessible points = 1.400000 m= 28559 mr = 50713 m= 5368 mr = 21555 m= 457 mr = 3480 m= 6 mr = 226 m= 0 mr = 2 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 29862 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 80 iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 15254 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) : 0.6956929 object centre at (A) : 2.431000 8.180000 22.45000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.9163169E-02 6.5311261E-02 midg,1,midg; midg,igrid,midg 2.4749450E-02 6.8155732E-03 1,midg,midg; igrid,midg,midg 5.1387544E-03 4.5624558E-02 gauss-seidel spectral radius is 0.9987914 estimated iterations to convergence 228 setup time was (sec) 0.5600000 now iterating at: 06:44:43 rms-change max change #iterations 4.406394 229.7214 at 10iterations 2.161366 77.16227 at 20iterations 1.058015 32.72043 at 30iterations 0.5219952 16.72644 at 40iterations 0.2555611 7.812059 at 50iterations 0.1260475 3.890041 at 60iterations 6.1812311E-02 2.115470 at 70iterations 3.0534899E-02 0.9302179 at 80iterations 1.5117728E-02 0.4605865 at 90iterations 7.5332643E-03 0.2729428 at 100iterations 3.8097030E-03 0.1155472 at 110iterations 1.9852242E-03 6.2568665E-02 at 120iterations finished qdiffx linear iterations at : 06:44:50 total time elapsed so far: 7.480000 # loops : 120 mean,max change (kT/e) : 1.9852242E-03 6.2568665E-02 energy calculations done at 7.480000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.610000 DelPhi exited at 06:44:51 7.616u 0.202s 0:08.23 94.8% 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 Tue Oct 11 2011 at 06:44:51 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2033 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 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= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.130618 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): -18.97500 23.83700 ymin,ymax (A): -12.31300 28.67300 zmin,zma (A): -3.136000 48.03600 x,y,z range (A): 42.81200 40.98600 51.17200 scale (grids/A): 3.130618 object centre (A): 2.431000 8.180000 22.45000 number of atom coordinates read : 2033 total number of charged atoms : 1923 net assigned charge : 6.931010 assigned positive charge : 311.3571 centred at (gu) : 88.79910 88.92408 91.88583 assigned negative charge : -304.4261 centred at (gu) : 87.99052 89.01360 91.93597 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 164570 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17159 grid for indexing accessible points = 1.400000 m= 89484 mr = 122027 m= 35867 mr = 74268 m= 10093 mr = 29312 m= 1957 mr = 7777 m= 198 mr = 1421 m= 5 mr = 115 m= 0 mr = 2 time to grow re-entrant surface = 0.5599999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.080000 number of dielectric boundary points 67252 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.160000 number of grid points assigned charge 15384 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) : 2.087079 object centre at (A) : 2.431000 8.180000 22.45000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3183393 0.7748674 midg,1,midg; midg,igrid,midg 0.2114463 3.7516594E-02 1,midg,midg; igrid,midg,midg 0.2020588 0.3952966 gauss-seidel spectral radius is 0.9992837 estimated iterations to convergence 295 setup time was (sec) 1.300000 now iterating at: 06:44:52 rms-change max change #iterations 9.910745 358.4632 at 10iterations 5.833375 132.1583 at 20iterations 3.438533 69.67309 at 30iterations 2.020438 44.60544 at 40iterations 1.182246 23.83400 at 50iterations 0.6919470 12.92583 at 60iterations 0.4048781 7.442902 at 70iterations 0.2364253 4.843887 at 80iterations 0.1379790 2.829142 at 90iterations 8.0768541E-02 1.442951 at 100iterations 4.7332589E-02 0.7840881 at 110iterations 2.7867844E-02 0.5246677 at 120iterations 1.6542165E-02 0.3122635 at 130iterations 1.0046389E-02 0.1998444 at 140iterations 6.2699215E-03 0.1234436 at 150iterations 4.0901811E-03 8.0612183E-02 at 160iterations 2.8342763E-03 5.9200287E-02 at 170iterations 2.0760160E-03 4.1172028E-02 at 180iterations finished qdiffx linear iterations at : 06:45:03 total time elapsed so far: 12.27000 # loops : 180 mean,max change (kT/e) : 2.0760160E-03 4.1172028E-02 energy calculations done at 12.27000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.40000 DelPhi exited at 06:45:04 12.404u 0.209s 0:12.89 97.7% 0+0k 0+0io 0pf+0w