one thing to keep in mind is that changing the LJ parameters for a given
atom doesn't just change that atom - it changes the underlying parameters
used by that atom. This means anything that shared those parameters (same
atom type, but also possibly other atom types) will also be changed. You
can see this by using the "printljmatrix" command in parmed. If you want to
change only a certain atom and not other atoms, you will first need to
split off that atom or atoms from others by making it have a new type. The
is done with the "addljtype" command. Then you can change parameters for
the atoms without affecting others. Also check your results by using the
printljmatrix command (supplying the mask for the atoms with changed
parameters).
On Tue, Sep 23, 2025 at 5:09 AM James Ross via AMBER <amber.ambermd.org>
wrote:
> Dear Amber community,
>
> I am making a co-solvent system with mono and disaccharides. My approach
> for monosaccharides is use parmed to change the Os - Os LJ potential, to
> induce inter-glycan repulsion at large distances using
> changeLJPair .%Os .%Os 10.0 0.0001
> This keeps the monosaccharides out of hbonding distance preventing
> aggregation at high concentrations. It appears to work quite well.
>
> I am now working on disaccharides. I chose the glycosidic linkage oxygen
> as my repulsive atom and tried using
> changeLJPair @%Os&@O3 @%Os&@O3 15.0 0.0001
> There is only one Os atom that is named O3, so I thought this would work.
> The only other Os atoms are named O5. What is strange to me (hopefully not
> to you) is that this works for one of the O5 atoms (on a second
> monosccharide of the disaccharide), so no repulsion is seen, however on the
> other O5 atom (the same residue as the O3 atom) the O5 is repelled and the
> glycan geometry is malformed.
> I tried negative selection with the same outcome.
> changeLJPair .%Os&!.O5 @%Os&!.O5 15.0 0.0001
>
> Does anyone know why this is the case and have a possible solution? I
> could try giving the O3_Os atom a completely differnent name but it would
> be nicer to get this working as the approach is simpler.
>
> Many thanks
>
>
> Dr James Ross
>
> EPSRC Synthetic Biology Research Fellow,
>
> School of Molecular and Cellular Biology,
>
> Astbury Building 7.107
>
> University of Leeds, UK
>
> [cid:8fa239b6-da61-4c1b-bf66-e201f5416288]<
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> >
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Received on Tue Sep 23 2025 - 07:00:02 PDT
