there are lots of questions here.. see below
>
> 1. What is the recommended procedure for using terminal capping groups
> (e.g., ACE, NME)
it depends on what you are building. if the input PDB has these already,
then it should work automatically (perhaps try "prepareforleap" in cpptraj
to help get the structures amber-ready)
if you don't have them already, then the need to be modeled, and Amber is
not really set up to model structures. Chimera might be a better options
if you are building from sequence, then just use the residue name as you
indicated above
> and for incorporating non-standard amino acid stereochemistry within
> AMBER-based workflows?
>
do you mean D amino acids? or stereochemistry for non-standard amino acids?
>
> 2. Is it possible to define additional capping groups beyond those
> provided by default?
yes, but you would want to follow the procedure for making a non-standard
residue, see the ambermd.org site for some help on that. for a cap, it does
have some differences, and there were recently discussed on this list. you
might try searching the archives to see those discussions (see ambermd.org,
there is a search tool).
> If so, can these be exported or converted for use in GROMACS? Since
> GROMACS supports only a limited set of caps for amber force fields, I’m
> wondering what the best practice is when AMBER offers capping groups that
> are not already available in GROMACS.
that depend on the details of the force field and if GROMACS supports
them... that is a better question for the GROMACS support group than here.
It is possible, but I don't know of specific issues you might run into with
capping groups in GROMACS.
>
>
> Thank you for your guidance.
>
> Best regards
>
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Received on Tue Dec 02 2025 - 09:00:03 PST
