Re: [AMBER] Problem regarding Chamber and psf file

From: Jason Swails <jason.swails.gmail.com>
Date: Thu, 21 Sep 2017 23:16:41 -0400

On Thu, Sep 21, 2017 at 4:45 PM, David Sáez <davidsaez.udec.cl> wrote:

> Hi Jason, I had some trouble using pmemd.cuda and a prmtop file originated
> by Parmed.
>
> I posted my problem here: http://archive.ambermd.org/201709/0308.html
>
> I think it is similar to this question: http://archive.ambermd.org/
> 201609/0398.html
>
> But in my case the hydrogen atom is in a HSD residue, not in a water
> molecule.
>
> Sorry to write directly to you, but could you give some advice?
>

​If a hydrogen is bonded to multiple atoms but is *not* in a rigid water
molecule (and this is on purpose), then you must either stop using SHAKE or
stop using pmemd.cuda.

HTH,
Jason


-- 
Jason M. Swails
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Received on Thu Sep 21 2017 - 20:30:02 PDT
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