[AMBER] Fwd: problem running with restraints

From: Sangeetha B <sangeetha.bicpu.edu.in>
Date: Thu, 11 Aug 2011 20:24:42 +0530

Hi,

Thanks for your suggestion...
But i tried it this way too...
If i use the group till 270, it works without any problem...
but when i include 289 to 558, i get the error...

Is it related only with the GPU memory?

My protein is a dimer and when i simulate as monomers (288 residues)
with the same restraints, it works properly...
I think i am doing something basically wrong... Please tell me where
should i look for correcting my error...

--
Sangeetha
Pondicherry University
On Tue, Aug 9, 2011 at 5:54 PM, case <case.biomaps.rutgers.edu> wrote:
> On Tue, Aug 09, 2011, Sangeetha B wrote:
>
>> Restraints
>> 2.0
>> RES 1 45
>> END
>> rest
>> 2.0
>> RES 59 134
>> END
>> rest
>> 2.0
>> RES 153 270
>> END
>> rest
>> 2.0
>> RES 289 333
>> END
>> rest
>> 3.0
>> RES 347 422
>> END
>> restr
>> 2.0
>> RES 441 558
>> END
>> END
>>
> I don't know if it will help the memory problem or not, but you can combine
> the above into a single group:
>
> Restraints
> 2.0
> RES 1 45 59 134 153 270 289 333 347 422 441 558
> END
> END
>
> It might be worth a try to see if that helps.....dac
>
> [If you really want 347 to 422 to have a slightly higher restraint(!?!), put
> those into a second group.]
>
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Received on Thu Aug 11 2011 - 08:00:05 PDT