[gmx-users] question on ffG43a1p force field

[Justin Lemkul]

On 8/18/19 3:24 AM, Lei Qian wrote:
> Could I ask one more question about your *gromos43a1p.ff* force filed ?
> Thanks!
> I ran $ gmx pdb2gmx -f myfile.pdb -o sort_processed.gro -water spce
>
> It shows a fatal error:
> "Fatal error:
> The residues in the chain xxx--xxx do not have a consistent type. The first
> residue has type 'Protein', while residue *SEP is of type 'Other'*.
> Either there is a mistake in your chain, or it includes nonstandard residue
> names that have not yet been added to the *residuetypes.dat file* in the
> GROMACS library directory."
>
> Then I found the *residuetypes.dat *in gromacs-2019.2/share/top, and add
> "SEP   protein" to the list.
> However, the fatal error still shows up after this change.
> Could I ask how to solve this problem?

You need to change the installed residuetypes.dat file, not the one in 
the source.

-Justin

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Justin A. Lemkul, Ph.D.
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