Re: [AMBER] Topological error for Mg in .prepin file.

From: ABEL Stephane <>
Date: Wed, 24 Oct 2018 13:41:03 +0000

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

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?



De : Anuja Ware []
Envoyé : mercredi 24 octobre 2018 15:22
À :
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
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