[gmx-users] charmm forcefield patches in gromacs

Mark Abraham mark.j.abraham at gmail.com
Mon Mar 31 11:18:29 CEST 2014

On Mar 29, 2014 7:29 AM, "Gurunath Katagi" <gurunath.katagi at gmail.com>
> Dear all,
> I want to do a simulation of protein containing phosphotyrosine using
> charmm forcefield (c32b1). A patch to obtain phosphotyrosine has been
> included in top_all27_prot_na_all.rtf file as TP2 (c32b1/toppar/stream
> But i see that, in the aminoacids.rtp this patches havent been included.
> there a way to include these patches into this forcefileld and run the
> simulation using gromacs.
> The obvious thing I can do is to add these patches as new residues and so
> on as given in the "how to add a resiude to forcefield ?
> Is there any alternative to include this patches . ?
> and also, can gromacs team care of including all other residues in the
> release.. ?

Very likely that would only happen if someone (not just an existing dev)
found themselves wanting to use more than one of them for a project.
However, if anyone did generate these new residues, they could freely share
them on the GROMACS contributions page. If they also made it easy to show
that they work (e.g. sample inputs and outputs for all cases) then we'd be
happy to consider them for a future release.


> thank you
> Gurunath
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