Sun Oct 9 02:13:36 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 02:13:36 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2463 !!! WARNING: HIT 84 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6480385 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): -121.3630 -67.85700 ymin,ymax (A): 46.40500 101.3400 zmin,zma (A): 63.54400 107.0240 x,y,z range (A): 53.50600 54.93501 43.48000 scale (grids/A): 0.6480385 object centre (A): -94.61000 73.87250 85.28400 number of atom coordinates read : 2463 total number of charged atoms : 2327 net assigned charge : 10.51402 assigned positive charge : 363.7182 centred at (gu) : 90.43400 88.77789 90.20752 assigned negative charge : -353.2050 centred at (gu) : 90.38494 88.79848 90.10542 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7094 nv = 96 ne = 84 npr = 48952 no. pairs analyzed = 48952 no. exposed pairs = 3295 no. arc points = 23528 no. surface atoms = 1096 nbur = 1367 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 420 mr = 3666 m= 2 mr = 38 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2700000 number of dielectric boundary points 3812 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2273 ## 229 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 8380 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.3230629E-09 3.3836720E-08 midg,1,midg; midg,igrid,midg 2.8092334E-08 1.2826566E-08 1,midg,midg; igrid,midg,midg 1.1580025E-08 2.7937372E-08 gauss-seidel spectral radius is 0.9876591 estimated iterations to convergence 74 setup time was (sec) 0.5200000 now iterating at: 02:13:37 rms-change max change #iterations 0.1502236 23.70483 at 10iterations 1.5257030E-02 2.108410 at 20iterations 1.7065373E-03 0.2345276 at 30iterations 3.1169900E-04 4.3039322E-02 at 40iterations 1.0265246E-04 1.6768873E-02 at 50iterations finished qdiffx linear iterations at : 02:13:40 total time elapsed so far: 3.270000 # loops : 50 mean,max change (kT/e) : 1.0265246E-04 1.6768873E-02 energy calculations done at 3.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.450000 DelPhi exited at 02:13:40 3.454u 0.224s 0:03.95 92.9% 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 Sun Oct 9 2011 at 02:13:40 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2463 !!! WARNING: HIT 84 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.944116 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): -121.3630 -67.85700 ymin,ymax (A): 46.40500 101.3400 zmin,zma (A): 63.54400 107.0240 x,y,z range (A): 53.50600 54.93501 43.48000 scale (grids/A): 1.944116 object centre (A): -94.61000 73.87250 85.28400 number of atom coordinates read : 2463 total number of charged atoms : 2327 net assigned charge : 10.51402 assigned positive charge : 363.7182 centred at (gu) : 91.30151 86.33339 90.62201 assigned negative charge : -353.2050 centred at (gu) : 91.15487 86.39540 90.31634 start vw surface at 0.1400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 75433 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23528 grid for indexing accessible points = 1.400000 m= 27618 mr = 50291 m= 4694 mr = 19769 m= 358 mr = 2738 m= 5 mr = 121 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 0.5400000 number of dielectric boundary points 35189 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 147 iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 18333 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) : 0.6480385 object centre at (A) : -94.61000 73.87250 85.28400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.4827025E-04 2.7162813E-02 midg,1,midg; midg,igrid,midg 4.2729098E-02 3.8785458E-02 1,midg,midg; igrid,midg,midg 2.1365751E-02 5.6404501E-02 gauss-seidel spectral radius is 0.9986891 estimated iterations to convergence 219 setup time was (sec) 0.8500000 now iterating at: 02:13:41 rms-change max change #iterations 4.211456 181.3177 at 10iterations 1.999583 73.32166 at 20iterations 0.9467399 32.40934 at 30iterations 0.4490144 15.06482 at 40iterations 0.2137474 6.811355 at 50iterations 0.1013630 3.416067 at 60iterations 4.8225697E-02 1.486428 at 70iterations 2.2985725E-02 0.6608758 at 80iterations 1.0942249E-02 0.3478384 at 90iterations 5.2055269E-03 0.1707821 at 100iterations 2.5047190E-03 7.3425293E-02 at 110iterations 1.2174564E-03 3.8742065E-02 at 120iterations finished qdiffx linear iterations at : 02:13:48 total time elapsed so far: 7.820000 # loops : 120 mean,max change (kT/e) : 1.2174564E-03 3.8742065E-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) 8.000000 DelPhi exited at 02:13:49 7.998u 0.271s 0:08.54 96.7% 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 02:13:49 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2463 !!! WARNING: HIT 84 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.916173 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): -121.3630 -67.85700 ymin,ymax (A): 46.40500 101.3400 zmin,zma (A): 63.54400 107.0240 x,y,z range (A): 53.50600 54.93501 43.48000 scale (grids/A): 2.916173 object centre (A): -94.61000 73.87250 85.28400 number of atom coordinates read : 2463 total number of charged atoms : 2327 net assigned charge : 10.51402 assigned positive charge : 363.7182 centred at (gu) : 91.95219 84.49993 90.93298 assigned negative charge : -353.2050 centred at (gu) : 91.73225 84.59312 90.47449 start vw surface at 0.1400000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 174358 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23528 grid for indexing accessible points = 1.400000 m= 87156 mr = 122663 m= 32828 mr = 69619 m= 8377 mr = 25749 m= 1447 mr = 5901 m= 122 mr = 899 m= 3 mr = 59 m= 0 mr = 0 time to grow re-entrant surface = 0.8100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.380000 number of dielectric boundary points 79401 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.540000 number of grid points assigned charge 18616 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) : 1.944116 object centre at (A) : -94.61000 73.87250 85.28400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.0341374E-02 0.2423624 midg,1,midg; midg,igrid,midg 0.4791796 0.7120439 1,midg,midg; igrid,midg,midg 0.3013465 0.5398165 gauss-seidel spectral radius is 0.9992813 estimated iterations to convergence 294 setup time was (sec) 1.730000 now iterating at: 02:13:51 rms-change max change #iterations 9.986397 307.5953 at 10iterations 5.957570 123.8552 at 20iterations 3.515894 73.57536 at 30iterations 2.067626 43.26007 at 40iterations 1.211705 23.38535 at 50iterations 0.7088820 14.76442 at 60iterations 0.4143214 7.839493 at 70iterations 0.2418358 4.837173 at 80iterations 0.1406585 2.620533 at 90iterations 8.1778489E-02 1.686670 at 100iterations 4.7549900E-02 0.8694367 at 110iterations 2.7636452E-02 0.4887993 at 120iterations 1.6078228E-02 0.3054128 at 130iterations 9.3494877E-03 0.1982002 at 140iterations 5.4458729E-03 9.6580505E-02 at 150iterations 3.1774619E-03 5.7369232E-02 at 160iterations 1.8633953E-03 3.5005569E-02 at 170iterations 1.1063988E-03 2.2871971E-02 at 180iterations finished qdiffx linear iterations at : 02:14:02 total time elapsed so far: 13.06000 # loops : 180 mean,max change (kT/e) : 1.1063988E-03 2.2871971E-02 energy calculations done at 13.06000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.23000 DelPhi exited at 02:14:03 13.236u 0.258s 0:13.76 97.9% 0+0k 0+0io 0pf+0w