Re: [AMBER] R: mm-pbsa calculation

From: Giulio Poli <giulio.poli.unipi.it>
Date: Wed, 28 Oct 2020 09:47:20 +0100

Hi Serena and Suchetana,

The error says that the surface arcs exceeded the limit, so it seems
that you have to increase the /maxarcdot/ value, that is the "maximum
number of arc dots required for solvent accessible surface".

Check this parameter on Amber manual: if you set /maxarcdot = 15000 /in
the /mmbsa.in /input file, you should solve the problem (if this is the
only problem of your calculation).

Hope this was useful.

Kindest regards,

Giulio

-- 
---
Giulio Poli, PhD
Research Scientist in Medicinal Chemistry
Department of Pharmacy University of Pisa
E-mail: giulio.poli.unipi.it
Il 28/10/2020 06:21, Suchetana Gupta ha scritto:
> 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
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>>
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Received on Wed Oct 28 2020 - 02:00:02 PDT