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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Sep 21 2017 - 20:30:02 PDT
