[gmx-users] atomtype "OE" in charmm36

[Justin Lemkul]

On 4/17/20 4:45 AM, Schirra, Simone wrote:
> Dear Gromacs users,
>
> I want to simulate polyethylene glycol and I am using a script to build my .itp and .gro files. The script is designed to work with charmm35r, however I only found charmm36 available now (I read, that c35r was only temporary). I thought, it should work with this version as well.
> When I try energy minimization, the atomtype OE is not found. OE is used for the ether oxygen's in the itp file.
> I also found an ether toppar file at MacKerell Lab Hompage, however it seems to be designed for use with charmm rather than gromacs.

Which toppar file are you trying to use?

> Is there a way to convert it for use with gromacs? Or is there another definition I can use to work with my PEG? Or maybe c35r is still somewhere around?

C35r became C36 in official implementation. Likely the atom type just 
got renamed or assumed into an existing one, but without knowing which 
topology you're using, I can't comment. The PEO "toppar_ether" from 
Alex's site doesn't have anything called OE in it.

-Justin

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Justin A. Lemkul, Ph.D.
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