Le 29/04/2014 17:30, Daniel Roe a écrit :
> Short answer is no. If you look at the form of the FF you can see that
> zero distance (i.e. complete overlap) leads to division by zero in
> non-bonded terms. You could potentially massage the minimizer by
> offsetting all the coordinates by different amounts and using very
> small initial steps, but it's probably more trouble than it's worth.
>
> -Dan
>
> On Tue, Apr 29, 2014 at 9:19 AM, Jean-Patrick Francoia
> <jeanpatrick.francoia.gmail.com> wrote:
>> Hello,
>>
>> I have a simple and quick question.
>>
>> Can Amber perform minimization if the pdb provided has no info about the
>> atoms coordinates ?
>> i. e let's admit we have something like that:
>>
>> ATOM 1 N LYS 1 0.000 0.000 0.000
>> ATOM 2 H1 LYS 1 0.000 0.000 0.000
>> ATOM 3 H2 LYS 1 0.000 0.000 0.000
>>
>> But all the residues are correctly numbered, and the atoms correctlt named.
>>
>> Regards
>>
>> _______________________________________________
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>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
Ok. At least I know it's not a solution to my problem. Thanks.
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Received on Tue Apr 29 2014 - 09:00:04 PDT
