Although I have not extensive experience, I would pay attention to this:
1) Terminal units of carbohydrate chains are properly set? Are saturated with OMe or OH groups?
2) When you have glycosilated proteins, the amino acid where carbohydrate chain is linked has a different name with respect to the "regular" one, and its charge is not integer, but this non - integer charge is balanced by the connecting carbohydrate unit. I remember that I asked this in the GLYCAM mailing list.
3) If you have branched carbohydrates, pay attention that the names and the connectivities are fine.
Hope this helps,
Tommaso
________________________________________
Da: David A Case [david.case.rutgers.edu]
Inviato: luned́ 12 novembre 2018 14.26
A: AMBER Mailing List
Oggetto: Re: [AMBER] leap warning: The unperturbed charge of the unit: -0.388000 is not integral, can I proceed for MD with such warning?
On Mon, Nov 12, 2018, maryam azimzadehirani wrote:
>The system is quite large... I have a dimer of two
>protein chains (each about 600 a.a). However the charge of the same system
>without glycans is integral.
Sounds like a question for the glycam mailing list, since it seems to be
related to the way you added sugars. Can you create a small example
that shows a non-integral charge, and post it to this list:
https://listserv.uga.edu/cgi-bin/wa?A0=GLYCAM-L
Although a small charge imbalance, per se, is not fatal, this message
could well be indicating that something else is wrong, so it's worth
investigating.
....dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Nov 12 2018 - 06:00:07 PST
