It looks likes this is an issue with the input parser for MMPBSA.py. The
parser is designed such that a comma indicates the end of one variable and
the start of the next variable. However, within AMBER, commas are used
between noncontinuous residues in a mask. Thus, for ptraj to correctly read
in your masks, the ptraj input files should have the receptor mask as
:1-468,509-510 and the ligand mask as :469-508. Until this gets fixed in the
code, a way for you to get around this would be to edit _MMPBSA_ptraj2.in
and _MMPBSA_ptraj3.in to have the correct masks as listed above. Then, you
can use the -use-mdins flag to read in all the input files as you have them,
instead of making new input files.
Good luck!
-Bill Miller
On Fri, Feb 12, 2010 at 10:09 AM, Arvind Marathe <bahuroopi.gmail.com>wrote:
> Hello,
>
> I am trying to calculate binding energy using the MMPBSA script. My
> receptor has two components, comprising of residues 1-468 and residues
> 509-510, while my ligand comprises of residues 569-508. I tested it on
> a trajectory file with 20 snapshots (containing receptor, ligand as
> well as solvent and ions). Following Jason Swails advice on
>
> http://archive.ambermd.org/201001/0220.html
>
> i used the following mask in my mmpbsa.in
>
>
> -------------------------------------------
> receptor_mask=':1-468:509-510', ligand_mask=':469-508',
> -------------------------------------------
>
> However, ptraj is not identifying the mask correctly. The mdcrd for
> the complex is formed correctly with all the 20 snapshots, as i can
> make out from the _MMPBSA_ptraj1.out file and the number of
> coordinates in _MMPBSA_complex.mdcrd file. But when it tried to
> extract the "ligand only" mdcrd by stripping the receptor, here are
> the relevant lines from _MMPBSA_ptraj2.out
>
> -------------------------------------------
> PTRAJ: strip :1-468:509-510
> Mask [:1-468:509-510] represents 7535 atoms
>
> PTRAJ: trajout _MMPBSA_ligand.mdcrd nobox
>
> PTRAJ: Successfully read the input file.
> Coordinate processing will occur on 23 frames.
> Summary of I/O and actions follows:
>
> INPUT COORDINATE FILES
> File (_MMPBSA_complex.mdcrd) is an AMBER trajectory with 23 sets
>
> OUTPUT COORDINATE FILE
> File (_MMPBSA_ligand.mdcrd) is an AMBER trajectory
>
> ACTIONS
> 1> STRIP: 7535 atoms will be removed from trajectory: :1-468
> -------------------------------------------
>
>
> As you can see, here ptraj goes entirely off the track. It only strips
> residues 1-468 (those contain 7535 atoms). But then it decides there
> are 23 snapshots in the trajectory, and goes on to extract only
> residues 469-470 (my guess, they comprise of 72 atoms, yet to confirm)
> in the _MMPBSA_ligand.mdcrd file. I have checked all my prmtop files
> again, and they are all correct.
>
> >From this point, everything goes wrong in the latter steps as well.
> Here are the relevant lines from _MMPBSA_ptraj3.out
>
>
> -------------------------------------------
> PTRAJ: trajin _MMPBSA_complex.mdcrd
>
> PTRAJ: strip :469-508
> Mask [:469-508] represents 72 atoms
>
> PTRAJ: trajout _MMPBSA_receptor.mdcrd nobox
>
> PTRAJ: Successfully read the input file.
> Coordinate processing will occur on 23 frames.
> Summary of I/O and actions follows:
>
> INPUT COORDINATE FILES
> File (_MMPBSA_complex.mdcrd) is an AMBER trajectory with 23 sets
>
> OUTPUT COORDINATE FILE
> File (_MMPBSA_receptor.mdcrd) is an AMBER trajectory
>
> ACTIONS
> 1> STRIP: 72 atoms will be removed from trajectory: :469,:470
> -------------------------------------------
>
>
> Finally, it fails with
>
>
> -------------------------------------------
> Error! Ptraj failed. Check coordinate and topology files for the complex.
> -------------------------------------------
>
>
> Using the suggestions from ambmask and ptraj sections in the amber
> manual, i tried different combinations for specifying the mask such as
>
>
> -------------------------------------------
> receptor_mask=':1-468,:509-510', ligand_mask=':469-508',
> or
> receptor_mask=':1-468,509-510', ligand_mask=':469-508',
> or
> receptor_mask=':1-468,509,510', ligand_mask=':469-508',
> or
> receptor_mask=":1-468,509,510", ligand_mask=":469-508",
> -------------------------------------------
>
>
> In each case, the script refuses to run with errors of the following type:
>
>
> -------------------------------------------
> :Warning: Input error! "509-510" is not recognized. Initialize
> variables with "="
> -------------------------------------------
>
>
> So how do i troubleshoot this problem? Is this problem only because of
> the mask, or there is some problem also in reading the
> parameter-topology file(s)?
>
> Any help appreciated.
>
> thanks,
> arvind
>
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>
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Received on Fri Feb 12 2010 - 08:00:02 PST
