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 - 07:00:02 PDT
