Sun Oct 9 16:03:20 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 16:03:20 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3045 !!! WARNING: GLM 254 has a net charge of -0.0940 !!! WARNING: MG9 970 has a net charge of 1.4000 !!! WARNING: MG9 971 has a net charge of 1.4000 !!! WARNING: MG9 972 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.6294090 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): -15.75500 37.01100 ymin,ymax (A): 3.380000 56.65500 zmin,zma (A): -34.64800 21.91300 x,y,z range (A): 52.76600 53.27500 56.56100 scale (grids/A): 0.6294090 object centre (A): 10.62800 30.01750 -6.367499 number of atom coordinates read : 3045 total number of charged atoms : 2897 net assigned charge : 2.606018 assigned positive charge : 455.1372 centred at (gu) : 90.50396 91.40548 88.64806 assigned negative charge : -452.5326 centred at (gu) : 90.55357 91.50940 88.59602 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 8035 nv = 96 ne = 84 npr = 62317 no. pairs analyzed = 62317 no. exposed pairs = 3717 no. arc points = 26328 no. surface atoms = 1261 nbur = 1784 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 476 mr = 4462 m= 3 mr = 61 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3991 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2551 ## 248 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 9849 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.0756404E-09 6.1832051E-09 midg,1,midg; midg,igrid,midg 9.8936068E-09 -1.0412424E-08 1,midg,midg; igrid,midg,midg 7.2029676E-09 -2.2335818E-09 gauss-seidel spectral radius is 0.9869642 estimated iterations to convergence 72 setup time was (sec) 0.5500000 now iterating at: 16:03:20 rms-change max change #iterations 0.1501292 21.36195 at 10iterations 1.4696040E-02 1.824096 at 20iterations 1.6079081E-03 0.2697144 at 30iterations 3.3595544E-04 6.5587997E-02 at 40iterations 1.1614796E-04 2.4253845E-02 at 50iterations finished qdiffx linear iterations at : 16:03:23 total time elapsed so far: 3.100000 # loops : 50 mean,max change (kT/e) : 1.1614796E-04 2.4253845E-02 energy calculations done at 3.100000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.270000 DelPhi exited at 16:03:23 3.273u 0.197s 0:03.75 92.2% 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 16:03:24 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3045 !!! WARNING: GLM 254 has a net charge of -0.0940 !!! WARNING: MG9 970 has a net charge of 1.4000 !!! WARNING: MG9 971 has a net charge of 1.4000 !!! WARNING: MG9 972 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.888227 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): -15.75500 37.01100 ymin,ymax (A): 3.380000 56.65500 zmin,zma (A): -34.64800 21.91300 x,y,z range (A): 52.76600 53.27500 56.56100 scale (grids/A): 1.888227 object centre (A): 10.62800 30.01750 -6.367499 number of atom coordinates read : 3045 total number of charged atoms : 2897 net assigned charge : 2.606018 assigned positive charge : 455.1372 centred at (gu) : 91.51124 94.21583 85.94336 assigned negative charge : -452.5326 centred at (gu) : 91.66055 94.52818 85.78796 start vw surface at 0.1800000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 87251 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26328 grid for indexing accessible points = 1.400000 m= 31053 mr = 60983 m= 5017 mr = 22703 m= 283 mr = 2986 m= 4 mr = 93 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6300000 number of dielectric boundary points 36843 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 162 iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 22722 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) : 0.6294090 object centre at (A) : 10.62800 30.01750 -6.367499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.4358034E-02 2.4443226E-02 midg,1,midg; midg,igrid,midg -5.1863100E-03 -1.2478495E-02 1,midg,midg; igrid,midg,midg -4.5814617E-03 -1.1908544E-02 gauss-seidel spectral radius is 0.9986510 estimated iterations to convergence 216 setup time was (sec) 0.9200000 now iterating at: 16:03:25 rms-change max change #iterations 4.596681 186.3450 at 10iterations 2.156244 79.94310 at 20iterations 1.016149 32.72152 at 30iterations 0.4756999 14.08609 at 40iterations 0.2247871 6.584885 at 50iterations 0.1054097 3.366250 at 60iterations 4.9552739E-02 1.556885 at 70iterations 2.3422150E-02 0.6814384 at 80iterations 1.1042915E-02 0.3319788 at 90iterations 5.2626734E-03 0.1678610 at 100iterations 2.5328002E-03 8.9534760E-02 at 110iterations 1.2477153E-03 4.1973114E-02 at 120iterations finished qdiffx linear iterations at : 16:03:31 total time elapsed so far: 7.570000 # loops : 120 mean,max change (kT/e) : 1.2477153E-03 4.1973114E-02 energy calculations done at 7.570000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.750000 DelPhi exited at 16:03:32 7.754u 0.203s 0:08.23 96.5% 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 Sun Oct 9 2011 at 16:03:32 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3045 !!! WARNING: GLM 254 has a net charge of -0.0940 !!! WARNING: MG9 970 has a net charge of 1.4000 !!! WARNING: MG9 971 has a net charge of 1.4000 !!! WARNING: MG9 972 has a net charge of 1.4000 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: 2.832340 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): -15.75500 37.01100 ymin,ymax (A): 3.380000 56.65500 zmin,zma (A): -34.64800 21.91300 x,y,z range (A): 52.76600 53.27500 56.56100 scale (grids/A): 2.832340 object centre (A): 10.62800 30.01750 -6.367499 number of atom coordinates read : 3045 total number of charged atoms : 2897 net assigned charge : 2.606018 assigned positive charge : 455.1372 centred at (gu) : 92.26676 96.32346 83.91499 assigned negative charge : -452.5326 centred at (gu) : 92.49095 96.79234 83.68193 start vw surface at 0.1400000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 202509 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26328 grid for indexing accessible points = 1.400000 m= 100757 mr = 148568 m= 36452 mr = 82006 m= 8962 mr = 28995 m= 1258 mr = 6592 m= 65 mr = 776 m= 1 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.9000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.500000 number of dielectric boundary points 83044 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.630000 number of grid points assigned charge 23175 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) : 1.888227 object centre at (A) : 10.62800 30.01750 -6.367499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2136488 0.3909793 midg,1,midg; midg,igrid,midg -0.2239776 -0.1201990 1,midg,midg; igrid,midg,midg -0.1505845 -0.1095700 gauss-seidel spectral radius is 0.9992711 estimated iterations to convergence 292 setup time was (sec) 1.800000 now iterating at: 16:03:34 rms-change max change #iterations 10.83710 372.9651 at 10iterations 6.372668 131.0205 at 20iterations 3.726095 76.84989 at 30iterations 2.177171 44.55382 at 40iterations 1.263158 26.37721 at 50iterations 0.7356712 13.48602 at 60iterations 0.4269190 7.440804 at 70iterations 0.2467870 5.257205 at 80iterations 0.1435231 2.796200 at 90iterations 8.2816906E-02 1.433231 at 100iterations 4.7939319E-02 0.8049698 at 110iterations 2.7732233E-02 0.4721451 at 120iterations 1.6075747E-02 0.2817917 at 130iterations 9.3228584E-03 0.1584015 at 140iterations 5.4402784E-03 0.1056118 at 150iterations 3.1989948E-03 6.2429428E-02 at 160iterations 1.9143281E-03 4.4418335E-02 at 170iterations 1.1856094E-03 2.4500847E-02 at 180iterations finished qdiffx linear iterations at : 16:03:45 total time elapsed so far: 12.76000 # loops : 180 mean,max change (kT/e) : 1.1856094E-03 2.4500847E-02 energy calculations done at 12.76000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.95000 DelPhi exited at 16:03:45 12.949u 0.253s 0:13.48 97.8% 0+0k 0+0io 0pf+0w