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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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Tue Apr 29 2014 - 09:00:02 PDT
