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GLYCAM-L  July 2017

GLYCAM-L July 2017

Subject:

Re: 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:

Wed, 26 Jul 2017 12:23:41 -0300

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (56 lines)

Hi David, 
thanks for your reply. I would be glad to give the new parameter set a shot on my system. I ran a quick simulation (10 ns) of the LIdopA[2S](2SO)a1-4DGlcpNS[6S]a1-4-OME using the residues OMe, UYS and 2uA (along with the proper sulfates) and adjusted the charges to those of 2uA2. Still I saw that most of the time the Irudonic ring would spend most of the time on a chair conformation. I imagined that I was missing some parameters other than the charges when building the system from 2uA. So I would deeply appreciate if along with the new parameter set you could also send me the prep files for 2uA2, so I can asses  the impact on the conformation of my molecule. 
Best regards, 
Cesar



----- Mensaje original -----
De: "David Thieker" <[log in to unmask]>
Para: [log in to unmask]
Enviados: MiƩrcoles, 26 de Julio 2017 11:26:11
Asunto: Re: Residue on parm file from gag builder missing in GLYCAM_06j-1.prep

Hi Cesar,

We have finished developing GLYCAM06k and are currently testing the files
to avoid any bugs. The new version of the IdoA residue type will be
included in this update, which should be released in the next week or so.
If you need the files sooner, I can send what we have. That would also help
us with the testing.

Just let me know how urgently you need them.

Best,
David

On Tue, Jul 25, 2017 at 6:35 PM, Cesar Avila <[log in to unmask]> wrote:

> 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
>



-- 
David F. Thieker
PhD Candidate
Biochemistry and Molecular Biology
Complex Carbohydrate Research Center
University of Georgia, Athens, GA

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