Hi,
There are many excellent basic and advanced tutorials for new and power users of Amber here : http://ambermd.org/tutorials/. In case of the mentioned papers you can download it here : https://onlinelibrary.wiley.com/doi/full/10.1002/jcc.10198 and or in researchgate (https://www.researchgate.net/publication/10976780_An_ab_initio_force_field_for_the_cofactors_of_bacterial_photosynthesis)
HTH
________________________________________
De : Anuja Ware [ware.anuja.p.gmail.com]
Envoyé : mercredi 24 octobre 2018 15:54
À : amber.ambermd.org
Objet : Re: [AMBER] Topological error for Mg in .prepin file.
Hello sir,
Sorry but I am unaware of that. Actually, I am new to amber and I am just
following tutorials. I don't know how to do that. Can u suggest me some
tutorial or method for the same as you have done? Please send me the link
of your publication.
On Wed, Oct 24, 2018 at 7:11 PM ABEL Stephane <Stephane.ABEL.cea.fr> wrote:
> Hello Anuja,
>
> I will not respond to your question but only add a comment about the
> bacteriochlorophyll a (Bcla) heme parameters . we have simulated the BclA
> with Amber previously w/o to derive the RESP charges and optimized the
> bonded parameters. Indeed the parameters of Ceccarelli et al. (DOI
> https://onlinelibrary.wiley.com/doi/full/10.1002/jcc.10198).
>
> Note that the charges were not derived according the AMBER procedure since
> they used DFT and the bonded parameter were taken from Amber94. But we
> obtained good results in our MD with them. Do you know them?
>
> HTH
>
> Stéphane
>
> ________________________________________
> De : Anuja Ware [ware.anuja.p.gmail.com]
> Envoyé : mercredi 24 octobre 2018 15:22
> À : amber.ambermd.org
> Objet : [AMBER] Topological error for Mg in .prepin file.
>
> Dear AMBER users,
> I am trying to generate a .lib file (parameters) for a non-standard
> residue, bacteriochlorophyll a. I have optimized the ring structure and
> derived RESP charges. Then I have run antechamber to generate .prepin
> file. But in prepin file the topological parameters of Mg atom are not
> clear. I get an error as follows:
>
> Atom X: Illegal chain specifier [0] in PREP file.
> 82 X 1 0 1 7.519 nan 0.000 0.000000
>
> What should one do in such type of case?
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Received on Wed Oct 24 2018 - 07:30:02 PDT
