Re: [AMBER] MM_PBSA not successful

From: Qinghua Liao <fantasticqhl.yahoo.com>
Date: Sat, 15 Aug 2009 07:55:40 +0100

Dear Sir, I am sorry I can't find the problem for you, wish others can help you! Good luck! Qinghua ________________________________ From: workalemahu berhanu <wgberhanu.gmail.com> To: AMBER Mailing List <amber.ambermd.org> Sent: Saturday, August 15, 2009 12:22:57 PM Subject: Re: [AMBER] MM_PBSA not successful Dear Qinghua I have below the output files . Thank you snapshot_com.all.out MM GB PB MS 1 BOND    =      205.9547  ANGLE  =      500.8292  DIHED      =      874.2771 VDWAALS =    -556.5644  EEL    =    -5494.9002  EGB        =    -1897.5408 1-4 VDW =      225.8409  1-4 EEL =      658.6870  RESTRAINT  =        0.0000 sander_com.in File generated by mm_pbsa.pl. Using  MM GB &cntrl   ntf    = 1,      ntb    = 0,      dielc  = 1.0,   idecomp= 0,   igb    = 2,      saltcon= 0.00,   offset = 0.09,   intdiel= 1.0,    extdiel= 80.0,   gbsa  = 0,      surften= 1.0,   cut    = 999.0,  nsnb  = 99999,   scnb  = 2.0,    scee  = 1.2,   imin  = 1,      maxcyc = 1,      ncyc  = 0, &end sander_lig.in File generated by mm_pbsa.pl. Using  MM GB &cntrl   ntf    = 1,      ntb    = 0,      dielc  = 1.0,   idecomp= 0,   igb    = 2,      saltcon= 0.00,   offset = 0.09,   intdiel= 1.0,    extdiel= 80.0,   gbsa  = 0,      surften= 1.0,   cut    = 999.0,  nsnb  = 99999,   scnb  = 2.0,    scee  = 1.2,   imin  = 1,      maxcyc = 1,      ncyc  = 0, &end sander_rec.in File generated by mm_pbsa.pl. Using  MM GB &cntrl   ntf    = 1,      ntb    = 0,      dielc  = 1.0,   idecomp= 0,   igb    = 2,      saltcon= 0.00,   offset = 0.09,   intdiel= 1.0,    extdiel= 80.0,   gbsa  = 0,      surften= 1.0,   cut    = 999.0,  nsnb  = 99999,   scnb  = 2.0,    scee  = 1.2,   imin  = 1,      maxcyc = 1,      ncyc  = 0, &end pbsa..in File generated by mm_pbsa.pl. Using PB &cntrl   ntf    = 1,      ntb    = 0,   igb    = 10,      dielc  = 1.0,   cut    = 999.0,  nsnb  = 99999,   scnb  = 2.0,    scee  = 1.2,   imin  = 1,      maxcyc = 0,      ntmin  = 2, &end &pb   epsin  = 1.0,    epsout  = 80.0,   istrng = 0,      radiopt = 0,   sprob  = 1.4,    space  = 0.5,   maxitn = 1000,    npopt  = 1,   cavity_surften = 0.0072,    cavity_offset  = 0.00,   npbverb= 1 &end mdinfo   NSTEP      ENERGY          RMS            GMAX        NAME    NUMBER       1      -5.4834E+03    1.8389E+01    1.0540E+02    CE2      636 BOND    =      205.9547  ANGLE  =      500.8292  DIHED      =      874.2771 VDWAALS =    -556.5644  EEL    =    -5494.9002  EGB        =    -1897.5408 1-4 VDW =      225.8409  1-4 EEL =      658.6870  RESTRAINT  =        0.0000 ~ On Fri, Aug 14, 2009 at 10:43 PM, Qinghua Liao<fantasticqhl.yahoo.com> wrote: > Dear Sir, > > If so, I think you should check the other output files to find some clues about the error. or you can show us those output files. > Good luck! > > Qinghua > > > > > ________________________________ > From: workalemahu berhanu <wgberhanu.gmail.com> > To: AMBER Mailing List <amber.ambermd.org> > Sent: Saturday, August 15, 2009 10:36:39 AM > Subject: Re: [AMBER] MM_PBSA not successful > > Dear Qinghua > > Hi > I introduced a line with fillratio=3.0 or 4.0 in the file pbsa.in. As > you explained in the mail archive > (http://archive.ambermd.org/200905/0326.html). The problem is still > there > > mikre.nid00235:~/PRION/MMPBSA> mm_pbsa.pl binding_energy..mmpbsa > > binding_energy.log >         /u0/z/zz217/USG/amber/9.0/exe/pbsa -O -i pbsa.in -o > pbsa_com.1.out -c ./snapshot_com.crd.1 -p ./GNNQQNYMYRSB.prmtop not > successful > > GNNQQNYMYRSB is the complex > > Thank you > > On Fri, Aug 14, 2009 at 9:20 PM, Qinghua Liao<fantasticqhl.yahoo.com> wrote: >> Hi, >> >> Maybe you should change the value of fillratio from default 2.0 to 3.0 or 4.0, you can have a try. >> >> Good luck! >> >> Qinghua >> >> >> >> >> ________________________________ >> From: workalemahu berhanu <wgberhanu.gmail.com> >> To: AMBER.ambermd.org >> Sent: Saturday, August 15, 2009 5:45:41 AM >> Subject: [AMBER] MM_PBSA not successful >> >> Dear Amber users >> >> I am not getting the results for mmpbsa calculation Calculate the >> binding free energy. Can anyone help me? >> I have >> given both my input and output files. >> This is my input >> .GENERAL >> PREFIX                snapshot >> PATH                  ./ >> COMPLEX              1 >> RECEPTOR              1 >> LIGAND                1 >> COMPT                ./GNNQQNYMYRSB.prmtop >> RECPT                ./GNNQQNYSB.prmtop >> LIGPT                ./MYR.prmtop >> GC                    0 >> AS                    0 >> DC                    0 >> MM                    1 >> GB                    2 >> PB                    1 >> MS                    1 >> NM                    0 >> .PB >> PROC                  2 >> REFE                  0 >> INDI                  1.0 >> EXDI                  80.0 >> SCALE                2 >> LINIT                1000 >> PRBRAD                1.4 >> ISTRNG                0..0 >> RADIOPT              0 >> NPOPT                1 >> CAVITY_SURFTEN        0.0072 >> CAVITY_OFFSET        0.00 >> SURFTEN              0.0072 >> SURFOFF              0.00 >> .MM >> DIELC                1.0 >> .GB >> IGB                  2 >> GBSA                  1 >> SALTCON              0.00 >> EXTDIEL              80.0 >> INTDIEL              1.0 >> SURFTEN              0.0072 >> SURFOFF              0.00 >> .MS >> PROBE                0.0 >> .PROGRAMS >> This is my Out put >> =>> Init data >>     Presuming executables of amber suite to be in /u0/z/zz217/USG/amber/9.0/exe >> >> =>> Reading input parameters >>     Found PREFIX => snapshot >>     Found PATH => ./ >>     Found COMPLEX => 1 >>     Found RECEPTOR => 1 >>     Found LIGAND => 1 >>     Found COMPT => ./GNNQQNYMYRSB.prmtop >>     Found RECPT => ./GNNQQNYSB.prmtop >>     Found LIGPT => ./MYR.prmtop >>     Found GC => 0 >>     Found AS => 0 >>     Found DC => 0 >>     Found MM => 1 >>     Found GB => 2 >>     Found PB => 1 >>     Found MS => 1 >>     Found NM => 0 >>     Found PROC => 2 >>     Found REFE => 0 >>     Found INDI => 1.0 >>     Found EXDI => 80.0 >>     Found SCALE => 2 >>     Found LINIT => 1000 >>     Found PRBRAD => 1.4 >>     Found ISTRNG => 0.0 >>     Found RADIOPT => 0 >>     Found NPOPT => 1 >>     Found CAVITY_SURFTEN => 0.0072 >>     Found CAVITY_OFFSET => 0.00 >>     Found SURFTEN => 0.0072 >>     Found SURFOFF => 0.00 >>     Found DIELC => 1.0 >>     Found IGB => 2 >>     Found GBSA => 1 >>     Found SALTCON => 0.00 >>     Found EXTDIEL => 80.0 >>     Found INTDIEL => 1.0 >>     Found SURFTEN => 0.0072 >>     Found SURFOFF => 0.00 >> Found PROBE => 0.0 >> Checking sanity >>     Checking GENERAL >>     Checking MM >>     Checking PB >>     Checking GB >>     Checking MS >> >> =>> Creating input >>     Sander input >>     PBSA input >> >> =>> Calculating energy / entropy contributions >>     Calc contrib for ./snapshot_com.crd..1 >>         Calc MM/GB/SAS >>         Generate PDB >>         Center PDB >>         Calc PBSA >> $AMBERHOME/exe/mm_pbsa..pl binding_energy.mmpbsa > binding_energy.log >>         /u0/z/zz217/USG/amber/9.0/exe/pbsa -O -i pbsa.in -o >> pbsa_com.1.out -c ./snapshot_com.crd.1 -p ./GNNQQNYMYRSB.prmtop not >> successful >> >> _______________________________________________ >> AMBER mailing list >> AMBER.ambermd.org >> http://lists.ambermd.org/mailman/listinfo/amber >> >> >> >> >> _______________________________________________ >> AMBER mailing list >> AMBER.ambermd..org >> http://lists.ambermd.org/mailman/listinfo/amber >> > > _______________________________________________ > AMBER mailing list > AMBER.ambermd..org > http://lists.ambermd.org/mailman/listinfo/amber > > > > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber > _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amber
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Received on Wed Aug 19 2009 - 22:36:07 PDT
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