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

From: maryam azimzadehirani <maryamai1988.gmail.com>
Date: Mon, 19 Mar 2018 12:01:35 +0100

Dear AMBER users,

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).

We discussed this in the group and guessed that maybe the difference is
coming from the charge alteration of glycosylated Asn (we have 2
glycosylated Asn in the system). To keep the file compatible with GLYCAM
forcefield I have changed glycosylated Asn to NLN and I tried to neutralize
the system. This time I get 5.7 NA+ ions to neutralize the system.

Which is very confusing... I are quite trapped at the moment and I
appreciate any help/ suggestion

Thank you

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Received on Mon Mar 19 2018 - 04:30:03 PDT
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