Thank you
On Sat, Dec 28, 2013 at 11:47 PM, Jason Swails <jason.swails.gmail.com>wrote:
> On Sat, Dec 28, 2013 at 4:40 AM, Asfa Ali <asfa.iisc.gmail.com> wrote:
>
> > Hi,
> >
> > Thank you so much for the suggestions.
> >
> > I checked the prmtop files that I created with the corresponding
> > inpcrd files and looked very fine in VMD. However when I am creating
> > the snapshots usinf extract_coord.mmpbsa, the crd files of the lig and
> > com are showing irregular bondings. I read a similar problem in
> > http://archive.ambermd.org/201103/0529.html.
> >
> > Plz tell me is there any other way to generate snapshots for mmpbsa
> > calculation.
> >
>
> You can always use cpptraj or ptraj instead, but that is what MMPBSA.py
> does behind the scenes. What you need to do is to understand exactly what
> the programs are doing to create the intermediate trajectories and why the
> programs do what they do. MMPBSA.py and mm_pbsa.pl are scripts designed
> to
> automate the procedure of carrying out MM/PBSA calculations, but they
> should _not_ be used as black boxes. As the manual explains, you should be
> able to carry out these calculations "by hand" and use the scripts only to
> automate your workflow after you understand the underlying technique.
>
>
> > Also as you suggested, when I am running MMPBSA.py, the following
> > errors are apperaing:
> >
> > Warning: igb=2 should be used with mbondi2 pbradii set. Yours are
> > modified Bondi radii (mbondi)
> >
> > Preparing trajectories with ptraj...
> > checkCoordinates(): Could not predict number of frames for AMBER
> > trajectory file: _MMPBSA_complex.mdcrd
> > If this is not a compressed file then there is a problem
> > checkCoordinates(): Could not predict number of frames for AMBER
> > trajectory file: _MMPBSA_complex.mdcrd
> > If this is not a compressed file then there is a problem
> > checkCoordinates(): Could not predict number of frames for AMBER
> > trajectory file: _MMPBSA_complex.mdcrd
> > If this is not a compressed file then there is a problem
> > 5 frames were read in and processed by ptraj for use in calculation.
> >
>
> This is the same problem you ran into with mm_pbsa.pl, and indicates that
> you are not creating the trajectories or the topology files correctly.
>
>
> >
> > Starting sander calls
> >
> > Starting gb calculation...
> >
> > bad atom type: K
> > bad atom type: K
> >
>
> Do you still have ions in your topology file? MMPBSA.py strips these out
> by default. You probably want to create topology files without explicit
> ions.
>
>
> > Starting pb calculation...
> >
> > Cannot match namelist object name cutcap
> > namelist read: misplaced = sign
> > Cannot match namelist object name 1
> > Cannot match namelist object name xcap
> > namelist read: misplaced = sign
> > [snip]
> >
>
> Something is seriously wrong here. Without knowing what your input files
> are, it's impossible to tell what happened. I would suggest doing the
> following:
>
> 1) Make sure you are using the most up-to-date version of AmberTools
> (version 13, updated to 13.22 -- you can use the command
> "$AMBERHOME/update_amber --version" to verify that AmberTools 13 is
> up-to-date).
>
> 2) Follow the MMPBSA.py tutorial at
> http://ambermd.org/tutorials/advanced/tutorial3 and be sure you can do
> each
> step on your own (and that you understand what each step is doing).
>
> 3) Try to adapt the input files from step (2) to your project in order to
> isolate your problems. If you continue having problems and ask for help on
> this list, you need to give details about what you tried, including the
> exact input files you used, the version of the software that you used, and
> the exact output of the programs that you ran.
>
> Good luck,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Asfa Ali
Prof. S. Bhattacharya's group,
Dept. of Organic Chemistry,
Indian Institute of Science,
Bangalore-12
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Received on Mon Dec 30 2013 - 14:00:04 PST
