[gmx-users] Charmm36M neutral C-terminal Proline

[Justin Lemkul]

On Tue, Aug 20, 2019 at 9:44 AM Akshay <akshays.sridhar at gmail.com> wrote:

> Hello All,
>
> I seem to be having a very particular issue with the Charmm36M force-field
> available at http://mackerell.umaryland.edu/charmm_ff.shtml. The issue
> occurs when using pdb2gmx's -ter flag and selecting a neutral COOH terminal
> when the C-terminal residue is a Proline.
>
> Then, when subsequent grompping, I get the two errors below where both
> lines pertain to the Proline backbone CA-C bond.
>
> ERROR 1 [file topol.top, line 493]:
>   No default U-B types
> ERROR 2 [file topol.top, line 649]:
>   No default Proper Dih. types
>
> Anyone else facing this issue or should I raise the issue with the 36M
> developers?
>

Given how rare such a combination would be, no one has invested time in
parametrizing this particular species. It’s simply not part of the force
field.

-Justin


> Thanks,
> Akshay
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-- 

==========================================

Justin A. Lemkul, Ph.D.

Assistant Professor

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Virginia Tech Department of Biochemistry
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