Keya,
Have you tried what the quoted error message says, "You can add implicit
radii using xparmed.py or parmed.py"? And then what happened?
Other than staying away from charmm stuff - nothing against the Charmmers,
but i'm an Amberist myself - you could follow one of the AMBER tutorials
and see that you can explicitly set the radii type using (at least) tLEaP.
Cheers,
Todd
On Mon, Mar 4, 2024 at 9:35 AM Joshi, Keya via AMBER <amber.ambermd.org>
wrote:
> Hello,
>
> I am trying to do MMGBSA analysis for a protein-peptide system. I
> extracted the complex.prmtop, receptor.prmtop and peptide.prmtop topology
> files from the step5_input.parm7 file.
>
> I run the mmgbsa analysis using this command line but I am getting this
> error-
>
> MMPBSA.py -O -i mmpbsa.in -o output.dat -sp step5_input.parm7 -cp
> com.prmtop -rp rec.prmtop -lp peptide.prmtop -y md-combined-all.nc
>
> PrmtopError: Topology files have no Implicit radii! You can add implicit
> radii using xparmed.py or parmed.py
>
> Fatal Error!
>
> Is there a way to add the implicit radii to the topology files? I also
> wanted to inform that I have prepared my system using charmm-gui with
> charmm36m forcefields and not amber forcefield.
>
> With Regards
> Keya Joshi
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>
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Received on Mon Mar 04 2024 - 09:00:02 PST
