Re: [AMBER] R: mm-pbsa calculation

From: Suchetana Gupta <tutulg.gmail.com>
Date: Wed, 28 Oct 2020 10:51:26 +0530

Hi Serena
I am sorry for the late response. I was on vacation.
I have never seen this error before. But my hunch is, it is similar to the
sander bomb error. However I am not sure how to solve this.
Did you manage to solve this? I'd love to stay updated regarding this.
Thanks
Suchetana

On Mon, Oct 19, 2020 at 3:06 PM Serena Vittorio <serena.vittorio.unime.it>
wrote:

> Hi Suchetana,
>
> thanks for your reply.
>
> I obtained the following message in the pbsa out file:
>
> SA Bomb in circle(): Stored surface arcs over limit
>
> Do you know what could be the problem?
>
> Thanks.
> Kind regards,
> Serena
>
>
>
> ________________________________
> Da: Suchetana Gupta <tutulg.gmail.com>
> Inviato: domenica 18 ottobre 2020 09:13
> A: AMBER Mailing List <amber.ambermd.org>
> Oggetto: Re: [AMBER] mm-pbsa calculation
>
> Hi Serena
> Can you please share the output or error file that is being generated? That
> could help.
> Thanks
> Suchetana
>
> On Fri, Oct 16, 2020 at 9:51 PM Serena Vittorio <serena.vittorio.unime.it>
> wrote:
>
> > Dear Amber users,
> >
> > I'm trying to perform mm-pbsa calculation, but I got the following
> message:
> >
> > /home/....../AMBER/amber18/bin/sander -O -i pbsa_com.in -o
> pbsa_com.1.out
> > -c ./cpd1_com.crd.1 -p complex.prmtop not successful
> >
> > What could be the cause and how can I fix it?
> >
> > Thanks in advance.
> > Serena
> >
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Received on Tue Oct 27 2020 - 22:30:02 PDT