Fwd: Re:

From: Branko (bdrakuli_at_chem.bg.ac.rs)
Date: Mon Jul 14 2014 - 13:24:43 CDT

jay,

You can add hydrogens in many programs.VMD
(http://www.ks.uiuc.edu/Research/vmd/) is native NAMD graphical user
interface. Also you could use VegaZZ (free
http://nova.disfarm.unimi.it/cms/index.php?Software_projects:VEGA_ZZ)
which have very user-friendly interface for addinig hydrogens. And
remember that majority of graphical user interfaces which allow you to
add hydrogens have propKa (http://propka.ki.ku.dk/) in background for
empirical estimation of protonation sates of ionizable sidechains
(probably you need protein in ionization state under physiological
conditions)

Branko

On 7/14/2014 8:05 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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