you have to source the glycam06 with leap and then you have to link the -OH (ROH) to the sialic acid (0SB or 0SA, depends if you wants alpha or beta anomer).
From: Users of GLYCAM & GLYCAM-Web [[log in to unmask]] on behalf of Manuel Maestre Reyna [[log in to unmask]]
Sent: Wednesday, June 08, 2016 1:13 AM
To: [log in to unmask]
Subject: parameters for neuraminic acid
Dear Glycam Users,
I'm sorry if this message gets posted twice, but I'm not quite sure how to use this mailing list yet.... I've previously sent it directly from my email, but can neither see it here in the archives, nor on my account. Either way, here it goes:
I'm trying to simulate a simple glycan with Amber 16, but it contains neuraminic acid (i.e. non-acetylated Neu5Ac). As far as I understand, there are no parameters for this in the glycam06 force field. I asked over at the Amber mailing list, and Lachele very helpfully told me about the glycam mailing list. She suggested that probably I only need the partial charges for the molecule. Does anyone perhaps have them, or can anyone help me in calculating them?
Thank you very much,