On Wed, Apr 20, 2016 at 7:04 AM, Cortopassi, Wilian <
wilian.cortopassi.chem.ox.ac.uk> wrote:
> Thank you very much Jason.
>
> Unfortunately, igb=0 and igb=6 are not available.
>
> The problem is that, for some of my molecules, I have fluorine atoms, which
> gives me a "bad atom type f" error when I run GBSA with idecomp. And MMPBSA
> calculations are very time consuming for pairwise decomposition.
>
> So I am not entirely sure how to perform pairwise decomposition with fluoro
> compounds.
>
> Is there any other way to get the Coulomb energy decomposed by residue
> along a MD with Amber?
>
Try using "--write-mdins" to generate mdin files, change gbsa=2 to gbsa=0
in all of the generated mdin files, then use the "--use-mdins" flag to run
with your modified input files.
The manual should describe this operation mode for MMPBSA.py.
An alternative is to google your error message and follow the instructions
for modifying the source code to eliminate this error.
HTH,
Jason
--
Jason M. Swails
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Received on Wed Apr 20 2016 - 12:00:03 PDT
