[gmx-users] Charmm27 and Charmm36 atomtypes assignments for polymer

[Justin Lemkul]

On 11/29/19 3:27 AM, Mijiddorj B wrote:
> Dear Justin,
>
> As you suggested, I generated the charmm36 parameter using cgenff for
> single unit with two capping groups. After that, I created 3 residues based
> on the parameter of cgenff including N-ter side, Middle, and C-ter side
> residues. However, the net charges of these residues are not equal to zero
> as -0.002, -0.004, and -0.002, respectively.
>
> 1. How can I adjust the charge of these residue?

Your model compound surely didn't have a net -0.008 charge, so make sure 
you're assigning charges correctly. Without seeing your actual residue 
definitions, there's nothing I (or anyone else) can suggest.

> 2. Is it possible to run simulation ignoring the grompp comments?

When grompp tells you there's a problem, don't ignore it. If you're 
trying to simply override these unphysical charges, your simulation will 
be useless because your model does not reflect reality.

-Justin

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Justin A. Lemkul, Ph.D.
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