Hi Jesper,
This is a limitation of how sander handles pairwise decomposition printing.
The only option that you have for printing out pairs is by specifying the
residues you want the pairs printed out for. However, it will print out
every possible pair for every residue you print out. There is no avoiding
this.
Hope this helps,
Jason
2011/2/1 Jesper Sørensen <lists.jsx.dk>
> Hi,
>
>
>
> I am trying to run a pair-wise decomp calculation in with MMPBSA.py, but I
> am having some problems figuring out the syntax for print_res”…”
>
>
>
> I want to know how each residue interacts with residue 328 (which is in the
> ligand), so I figured, print_res=”328; 1-323” would do the trick, but this
> results in a calculation of all pairs of interactions between residue 1 and
> the rest, residue 2 and the rest.
>
> Is there a better way to do it?
>
>
>
> I also tried print_res=”328”,
>
> But that didn’t give me what I wanted either.
>
>
>
>
>
> Best regards,
>
> Jesper Sørensen
>
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Tue Feb 01 2011 - 07:00:06 PST
