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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Received on Fri Feb 12 2010 - 07:30:02 PST
