Dear Billy,
On Fri, Feb 12, 2010 at 9:20 PM, Billy Miller III <brmilleriii.gmail.com> wrote:
> 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.
Thanks for your reply. Does not seem to work. Here is what i did:
I modified _MMPBSA_ligtraj.in to read:
-------------------------------------------
trajin _MMPBSA_complex.mdcrd
strip :1-468,509-510
trajout _MMPBSA_ligand.mdcrd nobox
-------------------------------------------
I issued the following command:
/data/apps/amber9_mvapich2/exe/MMPBSA.py -i mmpbsa.in -y
complex_test.mdcrd.gz -use-mdins
However, after the run, which ends with the same error as reported
previously, the _MMPBSA_ligtraj.in file reads:
-------------------------------------------
trajin _MMPBSA_complex.mdcrd
strip :1-468:509-510
trajout _MMPBSA_ligand.mdcrd nobox
-------------------------------------------
So looks like the input file is being rewritten by the script (unless
the command syntax above is wrong?). The rest of the errors are same
as reported in my previous mail. What next?
Btw, what beats me is ptraj's behaviour in the second and third steps.
In the first step, it correctly reads 20 sets of coordinates from the
input trajectory, strips the ions and solvent, and creates
_MMPBSA_complex.mdcrd file. I have checked this file again and again,
and it contains exactly 20 sets, minus the ions and solvent. In the
second run, using the same _MMPBSA_complex.mdcrd as input, ptraj
claims to read 23 sets of coordinates. Even if the mask is incorrect,
why or how is it reading 23 sets of coordinates? I believe for this
step, it uses the prmtop file for the complex without ions and
solvent, and i have tested it to be correct. So what is happening
here?
Thanks for any pointers.
Regards,
arvind
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Received on Fri Feb 12 2010 - 10:00:04 PST
