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
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Received on Sat Dec 28 2013 - 10:30:03 PST
