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GLYCAM-L  July 2017

GLYCAM-L July 2017

Subject:

Residue on parm file from gag builder missing in GLYCAM_06j-1.prep

From:

Cesar Avila <[log in to unmask]>

Reply-To:

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

Date:

Tue, 25 Jul 2017 18:35:42 -0400

Content-Type:

text/plain

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Parts/Attachments

text/plain (9 lines)

Hello all, 
I have recently prepared topology, parameter and configuration files for a heparin disaccharide using the GAG builder on the website as follows

LIdopA[2S](2SO)a1-4DGlcpNS[6S]a1-4-OME

Notice that for the irudonic ring I have selected to use the 2S0 configuration. As a result, I get a parm7 and pdb file with the irudonic residue named 2uA2 (instead of the 2uA residue that gets generated for a chair configuration). I want to use tleap to build my system from scratch, without using the parm7 file. Unfortunately, I cannot find the 2uA2 residue anywhere in the prep files that come with amber (or in the glycam webpage). I have noticed that the charges on the atoms is different between 2uA and 2uA2. I was wondering if you could help me find the prep file that is currently used by the GAG builder, so I can use it with tleap. 
Best regards, 

Cesar

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