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GLYCAM-L  May 2016

GLYCAM-L May 2016

Subject:

Re: GLYCAM parameters for Sialic Acid (to be loaded in leap)

From:

Elvis Martis <[log in to unmask]>

Reply-To:

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

Date:

Fri, 27 May 2016 23:27:02 -0400

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (55 lines)

Hi Oliver,
Thanks a ton for your help.
This was very trivial indeed.
Regards
Elvis.

On Fri, 27 May 2016 10:07:17 +0200, Oliver Grant <[log in to unmask]> wrote:

>Hi Elvis,
>
>*"However, there is an additional OH attached to C2 which has no names." *I
>assume you mean that in the 3D structure there is a reducing terminal
>oxygen, and you don't know what to name it in the PDB file? The oxygen
>should be named O1, the hydrogen HO1 and the residue as ROH.
>
>If you build DNeup5Aca2-OH on glycam.org/cb <http://www.glycam.org/cb> you
>can check the PDB file for what GLYCAM requires. The reducing terminal
>section looks like this:
>HETATM 1 HO1 ROH 1 5.998 8.375 -1.724 1.00 0.00
> H
>HETATM 2 O1 ROH 1 6.265 8.935 -2.457 1.00 0.00
> O
>HETATM 3 C2 0SA 2 7.667 9.136 -2.407 1.00 0.00
> C
>HETATM 4 C1 0SA 2 7.999 9.869 -1.055 1.00 0.00
> C
>... etc
>
>As long as the carbohydrate is linear (not branched) and you have the
>residues correctly named and in the appropriate order, there is no need to
>explicitly "link" them in tleap. Tleap will automatically bond sequential
>residues as it does for amino acids in proteins. If you had a branched
>carbohydrate, then you would insert TER cards at the branch points and use
>the "bond" command in tleap.
>
>
>Oliver
>
>On Fri, May 27, 2016 at 9:20 AM, Elvis Martis <[log in to unmask]>
>wrote:
>
>> Hello,
>> I am trying to simulate N8-neuraminidase bound to sialic acid in AMBER14.
>> In order to use GLYCAM_06j-1 paramters for sialic acid, I edited
>> everything necessary. For example, residue name was changed to "0SA" and
>> then the atom names were changed as per the atom names in "0SA". However,
>> there is an additional OH attached to C2 which has no names. As per Prof.
>> Case's suggestion in "AMBER Digest, Vol 1588, Issue 1:message 5" we must
>> link "0SA" to "ROH", this I am not clear how to do it.
>> Can someone help me here?
>> Thanks in Advance.
>> Regards
>> Elvis Martis
>>
>

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