I have checked the atom names and they were correct. After some more
changes, O5' is recognized but a phosphate oxygen is not.
Thank you
On Thu, Jan 26, 2017 at 9:57 AM, Qinghua Liao <scorpio.liao.gmail.com>
wrote:
> Hello,
>
> Maybe the atom name of O5' is O5* in the lib or prep file.
>
> You can have a check and modify it.
>
>
> All the best,
> Qinghua
>
> On 01/26/2017 03:54 PM, Paul Meister wrote:
> > Hello AMBER users,
> >
> > I am trying to run some MDs on a enzyme with a bound tRNA. I have tried
> to
> > get parameters for the 5' terminal base with a phosphate using prepgen
> and
> > the RED server, however there is always one atom that is not recognized,
> > O5', the oxygen linking phosphate to the ribose. Does anyone know how to
> > solve this problem or are there parameters for a terminal guanosine
> > 5'-phosphate?
> >
> > Thank you all,
> >
> > Paul
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jan 26 2017 - 08:00:06 PST
