Sat Oct 15 13:19:19 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 15 2011 at 13:19:19 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2561 !!! WARNING: SEP 142 has a net charge of -0.4750 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: 0.6496350 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): -6.372000 43.70800 ymin,ymax (A): 13.08300 67.88300 zmin,zma (A): -11.69600 41.46600 x,y,z range (A): 50.08000 54.80000 53.16200 scale (grids/A): 0.6496350 object centre (A): 18.66800 40.48300 14.88500 number of atom coordinates read : 2561 total number of charged atoms : 2417 net assigned charge : 6.525012 assigned positive charge : 387.7579 centred at (gu) : 89.32419 90.61295 90.10088 assigned negative charge : -381.2336 centred at (gu) : 89.41642 90.76376 90.08714 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 7173 nv = 96 ne = 84 npr = 51462 no. pairs analyzed = 51462 no. exposed pairs = 3070 no. arc points = 22053 no. surface atoms = 1051 nbur = 1510 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 397 mr = 3898 m= 2 mr = 56 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 3618 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2274 ## 229 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 8662 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0291910E-08 1.4885256E-08 midg,1,midg; midg,igrid,midg 3.0377151E-08 -1.1745342E-08 1,midg,midg; igrid,midg,midg 3.0082305E-08 -1.0150361E-09 gauss-seidel spectral radius is 0.9877188 estimated iterations to convergence 74 setup time was (sec) 0.5800000 now iterating at: 13:19:20 rms-change max change #iterations 0.1524980 21.54606 at 10iterations 1.5512955E-02 2.345754 at 20iterations 1.5927429E-03 0.2480774 at 30iterations 1.6608136E-04 2.4131775E-02 at 40iterations 1.7298218E-05 2.7503967E-03 at 50iterations finished qdiffx linear iterations at : 13:19:24 total time elapsed so far: 3.960000 # loops : 50 mean,max change (kT/e) : 1.7298218E-05 2.7503967E-03 energy calculations done at 3.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.200000 DelPhi exited at 13:19:24 4.203u 0.420s 0:05.68 81.3% 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 15 2011 at 13:19:24 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2561 !!! WARNING: SEP 142 has a net charge of -0.4750 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: 1.948905 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): -6.372000 43.70800 ymin,ymax (A): 13.08300 67.88300 zmin,zma (A): -11.69600 41.46600 x,y,z range (A): 50.08000 54.80000 53.16200 scale (grids/A): 1.948905 object centre (A): 18.66800 40.48300 14.88500 number of atom coordinates read : 2561 total number of charged atoms : 2417 net assigned charge : 6.525012 assigned positive charge : 387.7579 centred at (gu) : 87.97215 91.83821 90.30213 assigned negative charge : -381.2336 centred at (gu) : 88.24896 92.29129 90.26114 start vw surface at 0.1200000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 77668 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22053 grid for indexing accessible points = 1.400000 m= 27316 mr = 53597 m= 4470 mr = 20129 m= 345 mr = 2795 m= 2 mr = 159 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 1238 time to turn everything in is 0.6200000 number of dielectric boundary points 33121 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 134 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 19065 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) : 0.6496350 object centre at (A) : 18.66800 40.48300 14.88500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3181012E-02 -4.7557112E-03 midg,1,midg; midg,igrid,midg 4.1606296E-02 2.0851571E-02 1,midg,midg; igrid,midg,midg 1.5907649E-02 -1.4077944E-02 gauss-seidel spectral radius is 0.9986850 estimated iterations to convergence 218 setup time was (sec) 0.9100000 now iterating at: 13:19:26 rms-change max change #iterations 4.402070 225.5261 at 10iterations 2.088284 70.07622 at 20iterations 0.9909517 31.48914 at 30iterations 0.4704956 15.13815 at 40iterations 0.2224138 7.015122 at 50iterations 0.1052945 3.033260 at 60iterations 5.0086927E-02 1.494773 at 70iterations 2.3720318E-02 0.6972809 at 80iterations 1.1296467E-02 0.3690580 at 90iterations 5.3570825E-03 0.1548080 at 100iterations 2.5518322E-03 8.2178354E-02 at 110iterations 1.2097053E-03 3.7361026E-02 at 120iterations finished qdiffx linear iterations at : 13:19:37 total time elapsed so far: 9.480000 # loops : 120 mean,max change (kT/e) : 1.2097053E-03 3.7361026E-02 energy calculations done at 9.480000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.660000 DelPhi exited at 13:19:37 9.661u 0.498s 0:13.06 77.7% 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 15 2011 at 13:19:37 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2561 !!! WARNING: SEP 142 has a net charge of -0.4750 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: 2.923357 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): -6.372000 43.70800 ymin,ymax (A): 13.08300 67.88300 zmin,zma (A): -11.69600 41.46600 x,y,z range (A): 50.08000 54.80000 53.16200 scale (grids/A): 2.923357 object centre (A): 18.66800 40.48300 14.88500 number of atom coordinates read : 2561 total number of charged atoms : 2417 net assigned charge : 6.525012 assigned positive charge : 387.7579 centred at (gu) : 86.95799 92.75738 90.45299 assigned negative charge : -381.2336 centred at (gu) : 87.37338 93.43673 90.39165 start vw surface at 0.1200000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 179461 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22053 grid for indexing accessible points = 1.400000 m= 89231 mr = 129822 m= 31902 mr = 73095 m= 8083 mr = 25440 m= 1451 mr = 6052 m= 138 mr = 1050 m= 1 mr = 88 m= 0 mr = 0 time to grow re-entrant surface = 0.9500000 no. cavity mid-points inaccessible to solvent = 4582 time to turn everything in is 1.620000 number of dielectric boundary points 74720 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.770000 number of grid points assigned charge 19336 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) : 1.948905 object centre at (A) : 18.66800 40.48300 14.88500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2287294 -0.2706164 midg,1,midg; midg,igrid,midg 0.4994393 0.1579129 1,midg,midg; igrid,midg,midg 0.2210104 -0.2717614 gauss-seidel spectral radius is 0.9992722 estimated iterations to convergence 293 setup time was (sec) 1.970000 now iterating at: 13:19:40 rms-change max change #iterations 10.17092 406.6985 at 10iterations 5.924350 148.1985 at 20iterations 3.443948 68.15368 at 30iterations 2.000249 41.70881 at 40iterations 1.156978 23.80858 at 50iterations 0.6694346 11.76383 at 60iterations 0.3866673 7.325851 at 70iterations 0.2233122 3.967606 at 80iterations 0.1285313 2.259299 at 90iterations 7.4340887E-02 1.337396 at 100iterations 4.2852078E-02 0.7438760 at 110iterations 2.4696175E-02 0.4737577 at 120iterations 1.4249417E-02 0.2442589 at 130iterations 8.2198977E-03 0.1346235 at 140iterations 4.7502387E-03 8.4292412E-02 at 150iterations 2.7344772E-03 4.6785355E-02 at 160iterations 1.5793670E-03 2.7629614E-02 at 170iterations 9.1013144E-04 1.5716553E-02 at 180iterations finished qdiffx linear iterations at : 13:19:58 total time elapsed so far: 19.30000 # loops : 180 mean,max change (kT/e) : 9.1013144E-04 1.5716553E-02 energy calculations done at 19.30000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.47000 DelPhi exited at 13:19:59 19.477u 0.503s 0:21.16 94.3% 0+0k 0+0io 0pf+0w