Re: [AMBER] cpptraj doesn't read c4 term of LJ 12-6-4 potential

From: Daniel Roe via AMBER <>
Date: Wed, 29 Jun 2022 05:57:19 -0400


Support for reading/writing LENNARD_JONES_CCOEF read/write was added
in version 5.3.7. However, none of the native energy functions in
cpptraj support calculating the 12-6-4 potential yet. You may be able
to get it to work with 'esander' (if cpptraj was compiled with
libsander support) but this is untested.


On Wed, Jun 29, 2022 at 5:00 AM Giulia Sormani via AMBER
<> wrote:
> Good morning to everyone,
> To simulate the binding of an organic molecule to Zr4+ ion I am using the
> 12-6-4 LJ potential (on Amber20).
> I think that the c4 parameter is actually taken into account during the
> simulation, indeed in the section Potential Function of the output file of
> pmemd.cuda there is the flag "lj1264 = 1".
> However, when I load the topology file in cpptraj I get the following
> mistake:
> "Warning: Amber topology flag 'LENNARD_JONES_CCOEF' is unrecognized and
> will be skipped" .
> Can someone help me with this?
> I also have another question: is there a way to print the c4/r^4 energy
> component between two atoms along the simulation?
> I tried to search an action of cpptraj doing so, the pairwise action
> evaluates the vdw energy between group of atoms, but not the single
> components.
> best,
> Giulia
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Received on Thu Aug 04 2022 - 13:33:47 PDT
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