Sat Oct 8 16:15:53 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 16:15:53 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 = 2454 !!! WARNING: ASL 35 has a net charge of -0.1000 !!! WARNING: GLM 41 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6233912 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): -2.370000 45.05700 ymin,ymax (A): -15.34400 29.72900 zmin,zma (A): -18.82600 38.28100 x,y,z range (A): 47.42700 45.07300 57.10700 scale (grids/A): 0.6233912 object centre (A): 21.34350 7.192500 9.727501 number of atom coordinates read : 2454 total number of charged atoms : 2385 net assigned charge : 1.306002 assigned positive charge : 368.3348 centred at (gu) : 91.16588 88.70668 89.99966 assigned negative charge : -367.0298 centred at (gu) : 91.26372 88.85255 90.11425 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6424 nv = 96 ne = 84 npr = 48815 no. pairs analyzed = 48815 no. exposed pairs = 3153 no. arc points = 22071 no. surface atoms = 1065 nbur = 1389 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 345 mr = 3501 m= 2 mr = 50 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 0.2500000 number of dielectric boundary points 3220 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2184 ## 201 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 7955 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.9416794E-09 -6.9027588E-09 midg,1,midg; midg,igrid,midg 1.4749343E-08 -6.8384440E-09 1,midg,midg; igrid,midg,midg 6.0431153E-09 -7.4565625E-09 gauss-seidel spectral radius is 0.9866630 estimated iterations to convergence 71 setup time was (sec) 0.4700000 now iterating at: 16:15:54 rms-change max change #iterations 0.1242665 18.99728 at 10iterations 1.1726549E-02 1.730385 at 20iterations 1.0960603E-03 0.1695600 at 30iterations 1.0574778E-04 1.7404556E-02 at 40iterations 1.2318347E-05 1.7585754E-03 at 50iterations finished qdiffx linear iterations at : 16:15:56 total time elapsed so far: 3.050000 # loops : 50 mean,max change (kT/e) : 1.2318347E-05 1.7585754E-03 energy calculations done at 3.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.230000 DelPhi exited at 16:15:57 3.230u 0.219s 0:03.74 91.9% 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 16:15:57 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 = 2454 !!! WARNING: ASL 35 has a net charge of -0.1000 !!! WARNING: GLM 41 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.870173 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): -2.370000 45.05700 ymin,ymax (A): -15.34400 29.72900 zmin,zma (A): -18.82600 38.28100 x,y,z range (A): 47.42700 45.07300 57.10700 scale (grids/A): 1.870173 object centre (A): 21.34350 7.192500 9.727501 number of atom coordinates read : 2454 total number of charged atoms : 2385 net assigned charge : 1.306002 assigned positive charge : 368.3348 centred at (gu) : 93.49717 86.11907 89.99841 assigned negative charge : -367.0298 centred at (gu) : 93.79095 86.55739 90.34276 start vw surface at 0.1400000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 70163 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22071 grid for indexing accessible points = 1.400000 m= 23995 mr = 48540 m= 3586 mr = 17405 m= 181 mr = 2242 m= 2 mr = 65 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 732 time to turn everything in is 0.5000000 number of dielectric boundary points 29675 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 149 iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 18724 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) : 0.6233912 object centre at (A) : 21.34350 7.192500 9.727501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.6984915E-02 -1.7237667E-02 midg,1,midg; midg,igrid,midg 2.1288443E-02 -6.8724947E-03 1,midg,midg; igrid,midg,midg 6.4427187E-03 -3.9804030E-02 gauss-seidel spectral radius is 0.9985743 estimated iterations to convergence 210 setup time was (sec) 0.7800000 now iterating at: 16:15:58 rms-change max change #iterations 3.994461 169.6403 at 10iterations 1.827347 62.06014 at 20iterations 0.8479473 33.70437 at 30iterations 0.3910788 13.61412 at 40iterations 0.1804591 6.425475 at 50iterations 8.3031707E-02 2.572029 at 60iterations 3.8296856E-02 1.308109 at 70iterations 1.7725864E-02 0.6229267 at 80iterations 8.1718965E-03 0.2561607 at 90iterations 3.7726429E-03 0.1218371 at 100iterations 1.7381784E-03 5.6716919E-02 at 110iterations 8.0217369E-04 2.7891636E-02 at 120iterations finished qdiffx linear iterations at : 16:16:06 total time elapsed so far: 8.460000 # loops : 120 mean,max change (kT/e) : 8.0217369E-04 2.7891636E-02 energy calculations done at 8.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.650000 DelPhi exited at 16:16:06 8.651u 0.254s 0:09.22 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 Sat Oct 8 2011 at 16:16:06 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 = 2454 !!! WARNING: ASL 35 has a net charge of -0.1000 !!! WARNING: GLM 41 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: 2.805260 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): -2.370000 45.05700 ymin,ymax (A): -15.34400 29.72900 zmin,zma (A): -18.82600 38.28100 x,y,z range (A): 47.42700 45.07300 57.10700 scale (grids/A): 2.805260 object centre (A): 21.34350 7.192500 9.727501 number of atom coordinates read : 2454 total number of charged atoms : 2385 net assigned charge : 1.306002 assigned positive charge : 368.3348 centred at (gu) : 95.24570 84.17857 89.99745 assigned negative charge : -367.0298 centred at (gu) : 95.68642 84.83611 90.51421 start vw surface at 0.1400000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 162326 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22071 grid for indexing accessible points = 1.400000 m= 78963 mr = 118150 m= 27518 mr = 63702 m= 6537 mr = 22036 m= 817 mr = 4874 m= 43 mr = 520 m= 0 mr = 18 time to grow re-entrant surface = 0.7200000 no. cavity mid-points inaccessible to solvent = 2280 time to turn everything in is 1.230000 number of dielectric boundary points 66904 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.370000 number of grid points assigned charge 19077 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) : 1.870173 object centre at (A) : 21.34350 7.192500 9.727501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1725675 -0.2533116 midg,1,midg; midg,igrid,midg 0.1922995 -9.4081298E-02 1,midg,midg; igrid,midg,midg 6.4615160E-02 -0.5338324 gauss-seidel spectral radius is 0.9992420 estimated iterations to convergence 287 setup time was (sec) 1.540000 now iterating at: 16:16:08 rms-change max change #iterations 9.485195 367.7308 at 10iterations 5.531365 146.3180 at 20iterations 3.203117 71.86905 at 30iterations 1.855002 45.91318 at 40iterations 1.067922 22.21506 at 50iterations 0.6137038 12.55225 at 60iterations 0.3525143 7.737774 at 70iterations 0.2020097 3.794380 at 80iterations 0.1157067 2.175331 at 90iterations 6.6198014E-02 1.225454 at 100iterations 3.7890032E-02 0.7674217 at 110iterations 2.1623846E-02 0.4152527 at 120iterations 1.2368824E-02 0.2401810 at 130iterations 7.0716515E-03 0.1380386 at 140iterations 4.0405169E-03 7.5320244E-02 at 150iterations 2.3077196E-03 4.5269728E-02 at 160iterations 1.3173455E-03 2.4965286E-02 at 170iterations 7.5191050E-04 1.5003204E-02 at 180iterations finished qdiffx linear iterations at : 16:16:19 total time elapsed so far: 12.16000 # loops : 180 mean,max change (kT/e) : 7.5191050E-04 1.5003204E-02 energy calculations done at 12.16000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.34000 DelPhi exited at 16:16:19 12.341u 0.243s 0:12.87 97.7% 0+0k 0+0io 0pf+0w