[gmx-users] gromacs.org_gmx-users at maillist.sys.kth.se; jalemkul at vt.edu

[Justin Lemkul]

On 8/21/19 1:25 PM, Maryam Sadeghi wrote:
>   Hi All,
>
> I have created a crystal structure of 2 polymer chains (PEG) and I need to
> calculate the cohesive energy for my system using CHARMM36 FF. In this case
> my fix_mol2 file includes 2 ligands, to convert to str file I get the
> following error:
>
> readmol2 warning: non-unique atoms were renamed. Now processing molecule
> LIG ... attype warning: carbon radical, carbocation or carbanion not
> supported; skipped molecule.
>
> How can I fix this problem? Changing the ligand IDs and names does not
> help. I even tried to make 2 separate mol2 files for each chain in the
> crystal structure, but still get the same error while converting to str
> file...

As Dallas mentioned, this is not a GROMACS problem so it is not 
appropriate for this mailing list.

I replied in ResearchGate to your post on the same topic.

-Justin

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Justin A. Lemkul, Ph.D.
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