Re:

From: Kenno Vanommeslaeghe (kvanomme_at_rx.umaryland.edu)
Date: Mon Jul 14 2014 - 15:58:25 CDT

This list is not a substitute for an advisor. These are really the kind of
questions your advisor should be able to answer. If not, you need to
either switch advisor or research topic.

On 07/14/2014 02:05 PM, Eifler, Jay Q. (UMKC-Student) wrote:
> I cannot find a reference on how NAMD adds its hydrogens.
>
> Chimera fully explains for example.
>
>
> I also am wondering if I use another program to add hydrogens
>
> but then minimize my structure in NAMD doesn't that
>
> just readjust the hydrogens to NAMD's force field parameters?
>
>
> So then shouldn't we just use NAMD's add hydrogens facility
>
> rather than other methods to be consistent? I've noticed that
>
> neutral protonations just adjust back to the odd looking structure
>
> with a hydrogen apparently deleted.
>
>
> Maybe I have some confusion about the hydrogens. Also,
>
> I thought they were held rigid with SHAKE or something.
>

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