Re: [AMBER] Inconsistency with the number of counter ions required for neutralization

From: David A Case <>
Date: Mon, 19 Mar 2018 08:07:34 -0400

On Mon, Mar 19, 2018, maryam azimzadehirani wrote:
> I am preparing glycosylated and unglycosylated
> models of a receptor. while making the unglycosylated solvated model I
> need 4 NA+ to neutralize the system but when I am trying to
> solvate glycosylated proteins 3NA+ ions were required for
> neutralization (3.6 NA+ to be precise, and leap added 3 ions to the system,
> I am not sure why 3 and not 4).

You need to try to figure out why the charge is non-integral: add up the
charges of the glyocosylated residue by itself. If that is not an
integer, something is going wrong with that residue. We would need to
know details about how you prepared your system. (I could not follow the
discussion that led to one system having a net charge of -3.6, and
another a net charge of -5.7, for example).

You might consider asking your question at the GLYCAM site, since they
are most likely to be the people that will know what to do.

...good luck....dac

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Received on Mon Mar 19 2018 - 05:30:02 PDT
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