Sun Oct 9 07:04:47 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 Sun Oct 9 2011 at 07:04:47 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2001 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NDP 187 has a net charge of -3.0000 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: 0.6922299 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): -24.48000 25.65900 ymin,ymax (A): 1.222000 45.94600 zmin,zma (A): 2.452000 53.88000 x,y,z range (A): 50.13900 44.72400 51.42800 scale (grids/A): 0.6922299 object centre (A): 0.5895004 23.58400 28.16600 number of atom coordinates read : 2001 total number of charged atoms : 1862 net assigned charge : -2.499985 assigned positive charge : 299.6560 centred at (gu) : 89.37039 89.42406 89.02080 assigned negative charge : -302.1561 centred at (gu) : 89.30303 89.64944 88.97533 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6383 nv = 96 ne = 84 npr = 42719 no. pairs analyzed = 42719 no. exposed pairs = 2427 no. arc points = 17198 no. surface atoms = 825 nbur = 1176 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 357 mr = 3559 m= 3 mr = 52 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 57 time to turn everything in is 0.2700000 number of dielectric boundary points 3132 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1611 ## 148 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 7356 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.6566451E-08 4.0400089E-10 midg,1,midg; midg,igrid,midg 6.7415399E-08 -8.2487368E-08 1,midg,midg; igrid,midg,midg -4.2615010E-08 6.9259136E-09 gauss-seidel spectral radius is 0.9891208 estimated iterations to convergence 78 setup time was (sec) 0.4800000 now iterating at: 07:04:47 rms-change max change #iterations 0.1822383 31.89123 at 10iterations 2.1684811E-02 3.335543 at 20iterations 2.5395411E-03 0.3756332 at 30iterations 2.9972417E-04 4.1169643E-02 at 40iterations 3.4966677E-05 5.1879883E-03 at 50iterations finished qdiffx linear iterations at : 07:04:50 total time elapsed so far: 2.870000 # loops : 50 mean,max change (kT/e) : 3.4966677E-05 5.1879883E-03 energy calculations done at 2.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.040000 DelPhi exited at 07:04:50 3.041u 0.134s 0:03.45 91.8% 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 07:04:50 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2001 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NDP 187 has a net charge of -3.0000 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: 2.076690 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): -24.48000 25.65900 ymin,ymax (A): 1.222000 45.94600 zmin,zma (A): 2.452000 53.88000 x,y,z range (A): 50.13900 44.72400 51.42800 scale (grids/A): 2.076690 object centre (A): 0.5895004 23.58400 28.16600 number of atom coordinates read : 2001 total number of charged atoms : 1862 net assigned charge : -2.499985 assigned positive charge : 299.6560 centred at (gu) : 88.11133 88.27205 87.06243 assigned negative charge : -302.1561 centred at (gu) : 87.90900 88.94833 86.92599 start vw surface at 0.1600000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 68376 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17198 grid for indexing accessible points = 1.400000 m= 25296 mr = 47487 m= 4255 mr = 19075 m= 285 mr = 2794 m= 2 mr = 92 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 1441 time to turn everything in is 0.5100000 number of dielectric boundary points 28766 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 74 iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 14765 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) : 0.6922299 object centre at (A) : 0.5895004 23.58400 28.16600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.0252190E-02 2.6896058E-02 midg,1,midg; midg,igrid,midg 7.0380762E-02 -4.7494411E-02 1,midg,midg; igrid,midg,midg -5.4757699E-02 -1.5544442E-02 gauss-seidel spectral radius is 0.9987801 estimated iterations to convergence 227 setup time was (sec) 0.7700000 now iterating at: 07:04:51 rms-change max change #iterations 4.414616 237.3484 at 10iterations 2.140850 87.11359 at 20iterations 1.046137 34.26912 at 30iterations 0.5104606 16.06363 at 40iterations 0.2491566 7.808060 at 50iterations 0.1215278 4.217110 at 60iterations 5.9310883E-02 1.866768 at 70iterations 2.8987985E-02 0.9298706 at 80iterations 1.4167462E-02 0.4963665 at 90iterations 6.8829213E-03 0.2110519 at 100iterations 3.3715586E-03 0.1071930 at 110iterations 1.6473475E-03 5.5704117E-02 at 120iterations finished qdiffx linear iterations at : 07:04:57 total time elapsed so far: 6.700000 # loops : 120 mean,max change (kT/e) : 1.6473475E-03 5.5704117E-02 energy calculations done at 6.700000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.880000 DelPhi exited at 07:04:58 6.879u 0.162s 0:07.31 96.1% 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 Sun Oct 9 2011 at 07:04:58 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2001 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NDP 187 has a net charge of -3.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.115035 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): -24.48000 25.65900 ymin,ymax (A): 1.222000 45.94600 zmin,zma (A): 2.452000 53.88000 x,y,z range (A): 50.13900 44.72400 51.42800 scale (grids/A): 3.115035 object centre (A): 0.5895004 23.58400 28.16600 number of atom coordinates read : 2001 total number of charged atoms : 1862 net assigned charge : -2.499985 assigned positive charge : 299.6560 centred at (gu) : 87.16692 87.40807 85.59373 assigned negative charge : -302.1561 centred at (gu) : 86.86361 88.42246 85.38898 start vw surface at 0.1300000 fill in re-entrant regions at 0.7200000 boundary points on vw surface= 157946 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17198 grid for indexing accessible points = 1.400000 m= 80727 mr = 114690 m= 30480 mr = 66945 m= 7843 mr = 24911 m= 1299 mr = 6023 m= 81 mr = 859 m= 1 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 0.7000000 no. cavity mid-points inaccessible to solvent = 5048 time to turn everything in is 1.520000 number of dielectric boundary points 64918 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.650000 number of grid points assigned charge 14896 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) : 2.076690 object centre at (A) : 0.5895004 23.58400 28.16600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.8353743 1.021361 midg,1,midg; midg,igrid,midg 0.8199433 -0.4957307 1,midg,midg; igrid,midg,midg -0.4981570 -0.1699789 gauss-seidel spectral radius is 0.9992858 estimated iterations to convergence 295 setup time was (sec) 1.790000 now iterating at: 07:05:00 rms-change max change #iterations 9.907866 406.7969 at 10iterations 5.762184 116.5170 at 20iterations 3.343334 67.94228 at 30iterations 1.943234 35.64229 at 40iterations 1.126870 21.31203 at 50iterations 0.6534626 11.58420 at 60iterations 0.3783866 7.480281 at 70iterations 0.2188263 4.182612 at 80iterations 0.1271400 2.524889 at 90iterations 7.3494010E-02 1.435846 at 100iterations 4.2630948E-02 0.7700148 at 110iterations 2.4658313E-02 0.5176773 at 120iterations 1.4287868E-02 0.2625635 at 130iterations 8.2968110E-03 0.1490870 at 140iterations 4.7990950E-03 9.3959808E-02 at 150iterations 2.7837825E-03 5.2574158E-02 at 160iterations 1.6110111E-03 3.2871485E-02 at 170iterations 9.3325553E-04 1.7417908E-02 at 180iterations finished qdiffx linear iterations at : 07:05:09 total time elapsed so far: 11.07000 # loops : 180 mean,max change (kT/e) : 9.3325553E-04 1.7417908E-02 energy calculations done at 11.07000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.24000 DelPhi exited at 07:05:09 11.245u 0.167s 0:11.68 97.6% 0+0k 0+0io 0pf+0w