Thanks Jason for your answer. I tested removing the &ewald namelist and
setting igb=6 or igb=1 but I have the same issue. As it was a bit tricky
for me to prepare the inpcrd and prmtop homotrimer files, my objective
was to quickly tested them on a simple minimization. I finally hope to
launch a simulation on this complex in a solvent box. May be, it will
work directly with the box.
Best regards,
Baptiste
The objective is finally to launch a simulation in a solvent box.
Le 18/01/2012 15:08, Jason Swails a écrit :
> What happens when you remove the&ewald namelist completely and set igb=6
> instead? If that fixes it, do you really the distance-dependent
> dielectric? Can you use a Generalized Born implicit solvent method instead
> (or just vacuum, if handled with care)? I don't think that option is
> frequently tested since it's an unusual choice, especially when GB options
> are available and do a much better job at calculating solvation effects.
>
> HTH,
> Jason
>
> On Wed, Jan 18, 2012 at 6:22 AM, Baptiste Legrand<bap.legrand.gmail.com>wrote:
>
>> Dear all,
>>
>> I'm trying to minimize a homotrimer of small coupounds in vacuum with
>> amber10 but it fails. the out file have only these lines:
>> ------------------------------**-------------------------
>> Amber 10 SANDER 2008
>> ------------------------------**-------------------------
>> and the processor continue to work at full charge (99%).
>>
>> I used antechamber to create a prepin file and then a frcmod for the
>> monomer and I have any problem to launch a minimization step. So, starting
>> from these files, I created new prmtop and inpcrd files for a trimer using
>> xleap (I joined these files and the min.in script). On a display, the
>> complex is fine nevertheless the minimization fails.
>> Thanks in advance.
>>
>> Best regards,
>> Baptiste
>>
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>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>
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Received on Wed Jan 18 2012 - 07:00:03 PST
