It wasn't quite clear to me what you meant from your first email. However,
this email makes it more clear. See Adrian's response, it is the most
likely scenario.
Try visualizing the temporary trajectory files (_MMPBSA_complex.mdcrd) with
the corresponding topology files and see if anything looks drastically
wrong.
Good luck!
Jason
On Mon, Nov 15, 2010 at 10:40 AM, Jose Borreguero <borreguero.gmail.com>wrote:
> Thanks for the tip. I implemented these steps by I'm still having the same
> problem.
> These are the computed energies for the first conformation, as given in
> file
> _MMPBSA_complex_gb.mdout:
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1 1.0324E+14 2.5132E+13 1.7860E+15 HA2 1705
>
> BOND = 2222.4107 ANGLE = 6085.2529 DIHED =
> 4574.8302
> * VDWAALS = ************** EEL = -52263.5696 EGB =
> -8681.4534
> 1-4 VDW = 2664.7813 1-4 EEL = 29817.0487 RESTRAINT =
> 0.0000
> ESURF = 430.5994
>
> I don't have this problem for the receptor (_MMPBSA_receptor_gb.mdout) or
> ligand (_MMPBSA_ligand_gb.mdout)
>
> *_MMPBSA_receptor_gb.mdout:*
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1 -1.6549E+04 1.9138E+01 1.1354E+02 CB 646
>
> BOND = 1695.9831 ANGLE = 4668.8489 DIHED =
> 3514.6238
> VDWAALS = -4709.0919 EEL = -37827.8824 EGB =
> -7041.7999
> 1-4 VDW = 2033.8658 1-4 EEL = 20958.7822 RESTRAINT =
> 0.0000
> ESURF = 157.9190
>
> *_MMPBSA_ligand_gb.mdout:*
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1 -4.6648E+03 1.9499E+01 1.2670E+02 C 243
>
> BOND = 526.4276 ANGLE = 1416.4040 DIHED =
> 1060.2064
> VDWAALS = -1369.4285 EEL = -13851.2116 EGB =
> -1983.2964
> 1-4 VDW = 630.9154 1-4 EEL = 8858.2665 RESTRAINT =
> 0.0000
> ESURF = 46.9434
>
> -Jose
>
> On Mon, Nov 15, 2010 at 9:14 AM, Bill Miller III <brmilleriii.gmail.com
> >wrote:
>
> > Use the same input file you have here (after removing ntc=2) and use the
> > MMPBSA.py command line as you normally would, except place the
> -make-mdins
> > flag at the end of the command line. This will create all necessary mdin
> > files that will be used during the calculation, without actually running
> > the
> > calculation. Then go into the newly created mdin files (named
> > _MMPBSA_*.mdin) using your favorite text editor and add ntc=2 to the
> &cntrl
> > section of those mdin files. Finally, use the same command from earlier
> to
> > execute MMPBSA.py, except place the -use-mdins flag in place of the
> > -make-mdins flag. This will tell MMPBSA.py to use mdin files that have
> > already been created (and modified) as they are instead of having them
> made
> > again by MMPBSA.py. Note, do not change the names of the respective mdin
> > files because MMPBSA.py will only read in the mdin files with the names
> it
> > has already assigned to them. This also gives a lot more flexibility to
> the
> > user, but is also more prone to user errors that will not be caught by
> > MMPBSA.py. So take caution when using these flags with MMPBSA.py,
> >
> > Good luck!
> >
> > -Bill
> >
> > On Mon, Nov 15, 2010 at 9:01 AM, Jose Borreguero <borreguero.gmail.com
> > >wrote:
> >
> > > Dear Amber users,
> > >
> > > I'm having trouble using MMPBSA on a simulation that was carried out
> with
> > > rigid bonds involving hydrogens. The Van der Waals computed energy by
> > > MMPSBA
> > > is out of scale. I though of including the 'ntc=2' option in the
> > following
> > > mmpbsa.in file:
> > >
> > > *&general
> > > endframe=2525, verbose=1,
> > > entropy=0,
> > > ntc=2,
> > > /
> > > &gb
> > > igb=2, saltcon=0.100
> > > /
> > > &pb
> > > istrng=0.100, fillratio=2.0, scale=1.0
> > > /*
> > >
> > > Unfortunately, the option 'ntc=3' is not understood by the parser. Does
> > > anyone has an idea of how can I call for rigid bonds in MMPBSA ?
> > >
> > > Best regards,
> > > Jose M. Borreguero
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> > --
> > Bill Miller III
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Graduate Student
> > 352-392-6715
> > _______________________________________________
> > 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
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Mon Nov 15 2010 - 08:00:04 PST
