[gmx-users] Mismatch between gromacs and python-networkx versions

[Francesco Pietra]

This is to let you know, that the fixed .mol2 (got by first removing #
comments, as you indicated), the script cgenff_charmm2gmx.py works well
with the NetworkX 2x and charmm36-nov2018.ff. I still have to run gromacs
with them, but the content of the files looks like to be what was expected.
fp

thanks again

On Mon, Nov 26, 2018 at 3:57 PM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 11/25/18 9:10 AM, Francesco Pietra wrote:
> > This is my first post to gromacs, to which I came in the hope that FEP
> > simulations are more efficient than with other engines.
> >
> > I updated debian amd64 from stretch to buster in order to have the said
> > preferred gromacs 2018 (2016 on stretch). Now, to set up the system
> > (protein+ligands) I have networkx2.x, while 1.11.x (which was on stretch)
> > is required. Am I wrong, or there is really such a mismatch?. If so, how
> to
> > turn around? I have only one version of linux.
>
> GROMACS has no NetworkX requirement. If you're talking about the
> cgenff_charmm2gmx.py script, that's different. You need NetworkX 1.11
> for it to work. But that's not a GROMACS issue.
>
> -Justin
>
> --
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>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
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