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GLYCAM-L  June 2016

GLYCAM-L June 2016

Subject:

Re: charges for neuraminic acid

From:

Lee-Ping Wang <[log in to unmask]>

Reply-To:

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

Date:

Wed, 8 Jun 2016 09:58:53 -0700

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (36 lines)

Hi Manuel,

I’m also a relatively new user, but here’s the procedure I would try:

Inside tleap:
1) Set up a simulation of a Neu5AC monosaccharide in TIP3P water using the existing residues
2) Delete the acetyl group and replace the carbonyl carbon with an amine hydrogen
3) Set the amine hydrogen charge to neutralize the system
4) Rename the residue to something not already used by GLYCAM
5) Write out an amber .prep file for the new residue you just created

Using amber:
6) Run the simulation for ~20 ns and save ~50 snapshots of the monosaccharide in .pdb format

Using RED server (or a similar charge-fitting program):
7) Derive charges for the new, non-acetylated monosaccharide

Using a text editor:
8) Replace the charges in your .prep file with the new charges

Inside tleap:
9) Now set up the simulation you actually want

Thanks,

- Lee-Ping

> On Jun 8, 2016, at 1:07 AM, mmaestre <[log in to unmask]> wrote:
> 
> Dear Glycam users,
> 
> 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,
> 
> Manuel

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