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GLYCAM-L  April 2018

GLYCAM-L April 2018

Subject:

total charge is not 0

From:

Kanin Wichapong <[log in to unmask]>

Reply-To:

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

Date:

Tue, 24 Apr 2018 13:17:49 -0400

Content-Type:

text/plain

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Parts/Attachments

text/plain (16 lines)

Dear Sir,

I tried to generate the parameters for Fondaparinux (Arixtra), in which the sequence is D-GlcNS6S-α-(1,4)-D-GlcA-β-(1,4)-D-GlcNS3,6S-α-(1,4)-L-IdoA2S-α-(1,4)-D-GlcNS6S-OMe, by using GLYCAM web server.  First, I had the problems that residue UYS, QYS, and 6YS don't have parameters in the GLYCAM_06j-1.prep  file.  However, I found updated parameters for GLYCAM  (GLYCAM_06k.prep) and all parameters for these residues can be found in leaprc.GLYCAM_06k.  But then I have another problems during tleap (in AMBER), I got this warning about charges

ERROR: The unperturbed charge of the unit: -0.155000 is not integral
WARNING: The unperturbed charge of the unit: -0.155000 is not zero.


So, how to fix this problem or the parameters of Fondaparinux for running MD simulations in AMBER are available somewhere? I tried to find available parameters for this heparin but I couldn't find it. 

Any helps or suggestions will be very appreciated.

Thank you so much in advance.

Best Regards,
Kanin Wichapong

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