I just tried running antechamber with sqm or mopac7 (Amber11, ff99SB)
and I have the same errors with the protonated C-terminal COOH group. I
know that this is a quite unusual case... Thanks for any help.
All the best,
Baptiste
Le 08/11/2012 10:28, Baptiste Legrand a écrit :
> Thanks David. I have the same problem with ntt=3.
> I quickly tried with small natural dipeptides Ala-Phe:
> CH3O-Ala-Phe-COOH, CH3O-Ala-Phe-COOMe, CH3O-Ala-Phe-COO and I had the
> same issue during the SA only for the CH3O-Ala-Phe-COOH as expected.
>
> Best regards,
> Baptiste
>
>
>
> Le 07/11/2012 15:46, David A Case a écrit :
>> On Wed, Nov 07, 2012, Baptiste Legrand wrote:
>>
>>> During the
>>> calculations on a specific compound, the temperature is not controled
>>> and "vlimit exceeded" errors occured during the SA protocol and the
>>> system blow up for some structures:
>>>
>>> NSTEP = 1800 TIME(PS) = 10.900 TEMP(K) = 735.86 PRESS
>>> NSTEP = 2000 TIME(PS) = 11.000 TEMP(K) = 10363.98 PRESS
>>> NSTEP = 2200 TIME(PS) = 11.100 TEMP(K) = 7826.16 PRESS
>> You need to have enough temperature control to prevent getting
>> temperatures of
>> 10,000 degrees. I'd recommend trying ntt=3 for this. Note that
>> there is no
>> real equivalent of tautp then: you have to just change the target
>> temperature
>> as a function of time to get the temperature profile you want.
>>
>> (ntt=3 offers better temperature regulation, especially for smallish
>> systems,
>> or systems without explicit solvent. Note that it is quite common to
>> have to
>> experiment a bit with a simulated annealing input to get a
>> temperature vs.
>> time profile that is effective.)
>>
>> You may also have a problem with the COOH group, but try the above
>> first.
>>
>> ...good luck...dac
>>
>>
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>
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Received on Tue Nov 13 2012 - 08:00:02 PST
