On Wed, Jul 17, 2013 at 5:44 AM, Fernando Martín García <fmgarcia.cbm.uam.es
> wrote:
>
>
> Dear Amber users,
>
> I'm trying to perform a decomposition
> per-residue of my system (protein+DNA) using the following input file:
>
>
> Input file for running PB and GB
> &general
> endframe=10,
> verbose=1,
> /
> &gb
> igb=2, saltcon=0.100
> /
> &decomp
> idecomp=1,
> print_res="86"
>
Make sure you are printing at least one residue from the receptor and one
residue from the ligand. This should be fixed in the next version, but
may not be for yours.
Also, make sure that you apply all bug fixes (and I suggest using
AmberTools 13), otherwise you may get some ugly formatting in the output
file. Note that for AmberTools 12 and 13, the default output file is
CSV-formatted for easy viewing in a spreadsheet program (although setting
csv_format=0 in the &decomp section will fix this).
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Jul 17 2013 - 06:00:04 PDT
