Sun Oct 9 16:14:38 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 16:14:38 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 = 3150 !!! WARNING: GLM 240 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5989031 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): -15.09000 37.22100 ymin,ymax (A): -57.62400 -3.793000 zmin,zma (A): -7.164000 52.27800 x,y,z range (A): 52.31100 53.83100 59.44200 scale (grids/A): 0.5989031 object centre (A): 11.06550 -30.70850 22.55700 number of atom coordinates read : 3150 total number of charged atoms : 3002 net assigned charge : -4.593979 assigned positive charge : 467.6409 centred at (gu) : 90.16560 89.40154 91.75397 assigned negative charge : -472.2364 centred at (gu) : 90.23747 89.31509 91.79771 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7337 nv = 96 ne = 84 npr = 65390 no. pairs analyzed = 65390 no. exposed pairs = 3694 no. arc points = 26057 no. surface atoms = 1263 nbur = 1887 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 371 mr = 4026 m= 0 mr = 44 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 3638 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2655 ## 251 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 9312 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.3581690E-13 -5.5215104E-09 midg,1,midg; midg,igrid,midg -6.3679129E-09 1.5880250E-09 1,midg,midg; igrid,midg,midg 1.1755390E-09 -5.1084843E-09 gauss-seidel spectral radius is 0.9856150 estimated iterations to convergence 68 setup time was (sec) 0.4300000 now iterating at: 16:14:38 rms-change max change #iterations 0.1228557 18.81683 at 10iterations 1.0564913E-02 1.495720 at 20iterations 9.5907925E-04 0.1390324 at 30iterations 1.6371593E-04 3.4021378E-02 at 40iterations 5.8293321E-05 1.3135910E-02 at 50iterations finished qdiffx linear iterations at : 16:14:41 total time elapsed so far: 3.310000 # loops : 50 mean,max change (kT/e) : 5.8293321E-05 1.3135910E-02 energy calculations done at 3.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.450000 DelPhi exited at 16:14:42 3.454u 0.163s 0:03.88 93.0% 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 Sun Oct 9 2011 at 16:14:42 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3150 !!! WARNING: GLM 240 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.796709 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): -15.09000 37.22100 ymin,ymax (A): -57.62400 -3.793000 zmin,zma (A): -7.164000 52.27800 x,y,z range (A): 52.31100 53.83100 59.44200 scale (grids/A): 1.796709 object centre (A): 11.06550 -30.70850 22.55700 number of atom coordinates read : 3150 total number of charged atoms : 3002 net assigned charge : -4.593979 assigned positive charge : 467.6409 centred at (gu) : 90.49595 88.20396 95.26120 assigned negative charge : -472.2364 centred at (gu) : 90.71219 87.94511 95.39288 start vw surface at 0.1100000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 80605 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26057 grid for indexing accessible points = 1.400000 m= 27588 mr = 56226 m= 3943 mr = 19971 m= 152 mr = 2368 m= 0 mr = 49 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 38 time to turn everything in is 0.4000000 number of dielectric boundary points 33674 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 219 iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 23392 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) : 0.5989031 object centre at (A) : 11.06550 -30.70850 22.55700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.9183512E-03 -3.9392561E-04 midg,1,midg; midg,igrid,midg -1.9810878E-02 -1.4331003E-02 1,midg,midg; igrid,midg,midg -1.3167825E-02 -2.0243509E-02 gauss-seidel spectral radius is 0.9985169 estimated iterations to convergence 206 setup time was (sec) 0.6200000 now iterating at: 16:14:42 rms-change max change #iterations 4.232560 168.1635 at 10iterations 1.916568 61.31379 at 20iterations 0.8664322 27.06053 at 30iterations 0.3937492 12.29312 at 40iterations 0.1780280 5.676104 at 50iterations 8.1175260E-02 2.571609 at 60iterations 3.6856398E-02 1.119148 at 70iterations 1.6755635E-02 0.4972472 at 80iterations 7.6499931E-03 0.2196434 at 90iterations 3.5242399E-03 0.1105919 at 100iterations 1.6430991E-03 5.7363510E-02 at 110iterations 8.0025505E-04 2.8713226E-02 at 120iterations finished qdiffx linear iterations at : 16:14:49 total time elapsed so far: 7.740000 # loops : 120 mean,max change (kT/e) : 8.0025505E-04 2.8713226E-02 energy calculations done at 7.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.870000 DelPhi exited at 16:14:50 7.870u 0.193s 0:08.36 96.4% 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 16:14:50 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3150 !!! WARNING: GLM 240 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.695064 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): -15.09000 37.22100 ymin,ymax (A): -57.62400 -3.793000 zmin,zma (A): -7.164000 52.27800 x,y,z range (A): 52.31100 53.83100 59.44200 scale (grids/A): 2.695064 object centre (A): 11.06550 -30.70850 22.55700 number of atom coordinates read : 3150 total number of charged atoms : 3002 net assigned charge : -4.593979 assigned positive charge : 467.6409 centred at (gu) : 90.74381 87.30599 97.89158 assigned negative charge : -472.2364 centred at (gu) : 91.06821 86.91764 98.08919 start vw surface at 0.1000000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 187404 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26057 grid for indexing accessible points = 1.400000 m= 90886 mr = 137260 m= 31294 mr = 73695 m= 6736 mr = 24741 m= 716 mr = 4954 m= 19 mr = 449 m= 0 mr = 11 time to grow re-entrant surface = 0.5700001 no. cavity mid-points inaccessible to solvent = 142 time to turn everything in is 1.010000 number of dielectric boundary points 75945 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.100000 number of grid points assigned charge 24012 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) : 1.796709 object centre at (A) : 11.06550 -30.70850 22.55700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1595785 5.1086180E-02 midg,1,midg; midg,igrid,midg -0.2096019 -0.2592744 1,midg,midg; igrid,midg,midg -0.2748528 -0.2677058 gauss-seidel spectral radius is 0.9992361 estimated iterations to convergence 286 setup time was (sec) 1.240000 now iterating at: 16:14:51 rms-change max change #iterations 10.17487 266.1301 at 10iterations 5.922571 134.7543 at 20iterations 3.420468 73.86208 at 30iterations 1.959073 40.48483 at 40iterations 1.128151 21.36463 at 50iterations 0.6469225 15.59999 at 60iterations 0.3696444 7.240501 at 70iterations 0.2115900 3.855026 at 80iterations 0.1210846 2.418652 at 90iterations 6.9063611E-02 1.363979 at 100iterations 3.9460383E-02 0.7037544 at 110iterations 2.2517379E-02 0.4480586 at 120iterations 1.2841275E-02 0.2416482 at 130iterations 7.3408554E-03 0.1359372 at 140iterations 4.1795000E-03 7.6695442E-02 at 150iterations 2.3841762E-03 4.6133041E-02 at 160iterations 1.3608676E-03 2.4542809E-02 at 170iterations 7.7655894E-04 1.4587402E-02 at 180iterations finished qdiffx linear iterations at : 16:15:03 total time elapsed so far: 12.66000 # loops : 180 mean,max change (kT/e) : 7.7655894E-04 1.4587402E-02 energy calculations done at 12.66000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.80000 DelPhi exited at 16:15:03 12.801u 0.211s 0:13.26 98.1% 0+0k 0+0io 0pf+0w