From: Gianluca Interlandi (gianluca_at_u.washington.edu)
Date: Mon Jul 14 2014 - 13:26:57 CDT
NAMD does not add hydrogens. You have to use the psfgen plugin in VMD.
Gianluca
On Mon, 14 Jul 2014, 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.
>
>
>
-----------------------------------------------------
Gianluca Interlandi, PhD gianluca_at_u.washington.edu
+1 (206) 685 4435
http://artemide.bioeng.washington.edu/
Research Assistant Professor at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
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