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GLYCAM-L  May 2016

GLYCAM-L May 2016

Subject:

GLYCAM parameters for Sialic Acid (to be loaded in leap)

From:

Elvis Martis <[log in to unmask]>

Reply-To:

Users of GLYCAM & GLYCAM-Web <[log in to unmask]>

Date:

Fri, 27 May 2016 03:20:31 -0400

Content-Type:

text/plain

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text/plain (7 lines)

Hello,
I am trying to simulate N8-neuraminidase bound to sialic acid in AMBER14.
In order to use GLYCAM_06j-1 paramters for sialic acid, I edited everything necessary. For example, residue name was changed to "0SA" and then the atom names were changed as per the atom names in "0SA". However, there is an additional OH attached to C2 which has no names. As per Prof. Case's suggestion in "AMBER Digest, Vol 1588, Issue 1:message 5" we must link "0SA" to "ROH",  this I am not clear how to do it.
Can someone help me here?
Thanks in Advance. 
Regards
Elvis Martis

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