Thanks David and Lachele. I will follow your suggestion and I will get you back in case I need additional help.
I just wanted to use the standard parameters to reduce possible artefacts.
Best,
Paola
________________________________________
From: Lachele Foley [lf.list.gmail.com]
Sent: Wednesday, May 25, 2016 10:08 PM
To: AMBER Mailing List
Subject: Re: [AMBER] standard parameter for sialic acid
I just now saw this message and the one to glycam.gmail.com.
What Dave said is good. If you need additional help, just say so.
The oligosaccharides section in the Amber manual gives a pretty
detailed overview, but I'm happy to answer other questions you might
have.
On Wed, May 25, 2016 at 8:02 PM, David A Case <david.case.rutgers.edu> wrote:
> On Wed, May 25, 2016, Bisignano, Paola wrote:
>
>>
>> Actually I realized that there should be standard parameters for the
>> small molecule in the GLYCAM06. I downloaded the most recent version
>> of parameters from the glycam.org website and I went through the
>> nomenclature to search for the sialic acid, which is supposed to be 0SA
>> in the GLYCAM_06j-1.prep file.
>>
>> I do not know if I got the proper molecule, but actually I realized that
>> the molecule is missing one -OH group, so the number of atoms are in
>> fact 37, instead of 39.
>
> For a stand-alone sialic acid, you need to link 0SA to ROH. More info is
> given here:
>
> http://glycam.org/docs/forcefield/glycam-naming-2/
>
> (or in the glycam section of the Amber Reference Manual).
>
>> p.s. I tried to send an email at glycam.gmail.com but I did not get any answers
>
> See this link for accessing the glycam mailing list:
>
> http://glycam.org/docs/news/2015/05/14/a-mailing-list-for-glycam/
>
> However, Lachele regularly follows the Amber list, so you will probably get
> a better answer from her soon.
>
> ....dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Thu May 26 2016 - 12:30:02 PDT
