Sat Oct 8 16:06:03 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 Sat Oct 8 2011 at 16:06:03 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2298 !!! WARNING: ASL 705 has a net charge of -0.1000 !!! WARNING: GLM 711 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: 0.6470492 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): -1.762000 46.47700 ymin,ymax (A): -16.42400 29.17900 zmin,zma (A): -18.38300 36.63600 x,y,z range (A): 48.23900 45.60300 55.01900 scale (grids/A): 0.6470492 object centre (A): 22.35750 6.377500 9.126499 number of atom coordinates read : 2298 total number of charged atoms : 2226 net assigned charge : 3.806002 assigned positive charge : 343.1181 centred at (gu) : 90.54277 88.83960 90.27291 assigned negative charge : -339.3128 centred at (gu) : 90.59476 88.96381 90.31788 start vw surface at 0.1200000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 6602 nv = 96 ne = 84 npr = 45638 no. pairs analyzed = 45638 no. exposed pairs = 2919 no. arc points = 20572 no. surface atoms = 996 nbur = 1302 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 377 mr = 3595 m= 2 mr = 43 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 0.2400000 number of dielectric boundary points 3343 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1992 ## 177 charges are in solution ## iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 7817 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1467520E-08 1.1043936E-09 midg,1,midg; midg,igrid,midg 2.7848808E-08 -6.8472166E-09 1,midg,midg; igrid,midg,midg 1.1601967E-08 1.6240215E-10 gauss-seidel spectral radius is 0.9876009 estimated iterations to convergence 73 setup time was (sec) 0.4900000 now iterating at: 16:06:04 rms-change max change #iterations 0.1451199 21.71784 at 10iterations 1.4761463E-02 2.588587 at 20iterations 1.5224639E-03 0.1906228 at 30iterations 1.7275712E-04 2.4504185E-02 at 40iterations 2.7656652E-05 4.3201447E-03 at 50iterations finished qdiffx linear iterations at : 16:06:07 total time elapsed so far: 3.150000 # loops : 50 mean,max change (kT/e) : 2.7656652E-05 4.3201447E-03 energy calculations done at 3.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.320000 DelPhi exited at 16:06:07 3.328u 0.239s 0:03.87 91.7% 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 Sat Oct 8 2011 at 16:06:07 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2298 !!! WARNING: ASL 705 has a net charge of -0.1000 !!! WARNING: GLM 711 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: 1.941148 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): -1.762000 46.47700 ymin,ymax (A): -16.42400 29.17900 zmin,zma (A): -18.38300 36.63600 x,y,z range (A): 48.23900 45.60300 55.01900 scale (grids/A): 1.941148 object centre (A): 22.35750 6.377500 9.126499 number of atom coordinates read : 2298 total number of charged atoms : 2226 net assigned charge : 3.806002 assigned positive charge : 343.1181 centred at (gu) : 91.62782 86.51842 90.81858 assigned negative charge : -339.3128 centred at (gu) : 91.78423 86.89142 90.95347 start vw surface at 0.1200000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 70529 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20572 grid for indexing accessible points = 1.400000 m= 26132 mr = 48439 m= 4714 mr = 19253 m= 309 mr = 3075 m= 3 mr = 133 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 437 time to turn everything in is 0.5100000 number of dielectric boundary points 30787 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 115 iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 17535 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) : 0.6470492 object centre at (A) : 22.35750 6.377500 9.126499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.1300768E-02 -5.2045104E-03 midg,1,midg; midg,igrid,midg 2.6179820E-02 -3.9022150E-03 1,midg,midg; igrid,midg,midg 1.0123410E-02 -4.4745177E-02 gauss-seidel spectral radius is 0.9986603 estimated iterations to convergence 216 setup time was (sec) 0.8100000 now iterating at: 16:06:08 rms-change max change #iterations 4.135221 184.6354 at 10iterations 1.944106 70.90245 at 20iterations 0.9188988 34.86053 at 30iterations 0.4337338 13.24368 at 40iterations 0.2042967 6.824673 at 50iterations 9.6887320E-02 3.027382 at 60iterations 4.5691431E-02 1.342224 at 70iterations 2.1601709E-02 0.6629968 at 80iterations 1.0191537E-02 0.3274536 at 90iterations 4.8045069E-03 0.1495070 at 100iterations 2.2807601E-03 7.3720992E-02 at 110iterations 1.0819676E-03 3.7164927E-02 at 120iterations finished qdiffx linear iterations at : 16:06:15 total time elapsed so far: 7.480000 # loops : 120 mean,max change (kT/e) : 1.0819676E-03 3.7164927E-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) 7.640000 DelPhi exited at 16:06:16 7.644u 0.255s 0:08.18 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 Sat Oct 8 2011 at 16:06:16 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2298 !!! WARNING: ASL 705 has a net charge of -0.1000 !!! WARNING: GLM 711 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: 2.911721 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): -1.762000 46.47700 ymin,ymax (A): -16.42400 29.17900 zmin,zma (A): -18.38300 36.63600 x,y,z range (A): 48.23900 45.60300 55.01900 scale (grids/A): 2.911721 object centre (A): 22.35750 6.377500 9.126499 number of atom coordinates read : 2298 total number of charged atoms : 2226 net assigned charge : 3.806002 assigned positive charge : 343.1181 centred at (gu) : 92.44152 84.77747 91.22771 assigned negative charge : -339.3128 centred at (gu) : 92.67642 85.33707 91.43003 start vw surface at 0.1300000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 163090 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20572 grid for indexing accessible points = 1.400000 m= 83419 mr = 117751 m= 31845 mr = 67968 m= 8635 mr = 25699 m= 1360 mr = 6640 m= 107 mr = 914 m= 4 mr = 66 m= 0 mr = 0 time to grow re-entrant surface = 0.7600000 no. cavity mid-points inaccessible to solvent = 1477 time to turn everything in is 1.300000 number of dielectric boundary points 69422 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.430000 number of grid points assigned charge 17807 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) : 1.941148 object centre at (A) : 22.35750 6.377500 9.126499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1854715 -9.7487122E-02 midg,1,midg; midg,igrid,midg 0.1914931 -6.2923841E-02 1,midg,midg; igrid,midg,midg 0.1131573 -0.6049297 gauss-seidel spectral radius is 0.9992675 estimated iterations to convergence 292 setup time was (sec) 1.620000 now iterating at: 16:06:17 rms-change max change #iterations 9.621309 407.6931 at 10iterations 5.653227 130.9328 at 20iterations 3.294401 64.16574 at 30iterations 1.923636 38.50650 at 40iterations 1.115740 20.00500 at 50iterations 0.6477270 15.62081 at 60iterations 0.3758852 7.497246 at 70iterations 0.2168417 4.774191 at 80iterations 0.1255918 2.666218 at 90iterations 7.2627693E-02 1.351337 at 100iterations 4.1893803E-02 0.8504181 at 110iterations 2.4181057E-02 0.4725107 at 120iterations 1.3969604E-02 0.2488599 at 130iterations 8.0340123E-03 0.1450405 at 140iterations 4.6454626E-03 8.1504822E-02 at 150iterations 2.6693798E-03 4.9145699E-02 at 160iterations 1.5406145E-03 2.7325630E-02 at 170iterations 8.8873773E-04 1.7236710E-02 at 180iterations finished qdiffx linear iterations at : 16:06:28 total time elapsed so far: 12.42000 # loops : 180 mean,max change (kT/e) : 8.8873773E-04 1.7236710E-02 energy calculations done at 12.42000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.60000 DelPhi exited at 16:06:29 12.601u 0.263s 0:13.15 97.7% 0+0k 0+0io 0pf+0w