Thanks for the tip. I tried to visualize the trajectory and it didn't work.
However, the problem wasn't the topology file, but the trajectory format. I
used ptraj to 'translate' the trajectory from dcd to ascii. MMPBSA didn't
give me trouble with the ascii trajectory.
I had created the dcd trajectory with ACEMD, instead of with AMBER. I assume
that dcd trajectories created with AMBER will not produce the trouble I got.
Thank you all for your suggestions!!!
- Jose
On Mon, Nov 15, 2010 at 10:47 AM, Jason Swails <jason.swails.gmail.com>wrote:
> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Nov 15 2010 - 08:30:05 PST
