Re: [AMBER] glycam - leap error

From: Karl N. Kirschner <>
Date: Fri, 13 Sep 2013 16:09:45 +0200 (CEST)

Hello lara lara,

  Following up on Lachele's suggestion, you can check the performance of the borrowed parameter using Wolf2Pack (W2P). One molecule (i.e. N_2-methoxyethyl_acetamide) already exists in W2P's database that could be a test molecule for Os-Cg-Cg-Ng's rotation behavior. You can compare the performance of the parameter versus B3LYP/B3LYP/6-311++G(2d,2p)//HF/6-31G(d) relative energy curves, which is how Glycam06 was developed.

  However, there are two things to consider if you choose to try this. 1) W2P uses an older version of Glycam (i.e. Glycam06g-1), before the atom types were changed to a mix of upper and lowercase letters. Thus, if you wanted to change the parameters, you would need to modify those associated with the N-CG-CG-OS torsion. 2) There are no protein parameters (e.g. H-N-C-O parameter) present in Glycam06g-1. Thus, you will have to supply them in the parameter file at the last stage of W2P's workflow. W2P uses the rules associated with the older version of leap, meaning that there is one uniform scaling factor (i.e. 1.0 for Glycam) for all parameter. This is not ideal since the protein parameter use scaling factors of 1.2 and 2.0, but it might be better than nothing. At least it would give you "sense" if the borrowed parameters are trustworthy or not.

  If you get stuck using W2P, let me know. There are several W2P tutorial and force-field information pages on the W2P server that you may find helpful to start out with if you are new to these ideas.

Best regards,

----- Original Message -----
From: "Lachele Foley" <>
To: "AMBER Mailing List" <>
Sent: Thursday, September 12, 2013 11:44:50 PM
Subject: Re: [AMBER] glycam - leap error

We don't have a parameter that has been validated for that linkage.
But, there is something you can use. It should work reasonably well,
but if you can find some way to validate it, that would be ideal.

The suggestion is to use the Os-Cg-Cg-Ng term for Os-Cg-Cg-N. This is
analogous to the treatment for Oh-Cg-Cg-Ng and Oh-Cg-Cg-N, so it has

If you want to do that, just copy the "Os-Cg-Cg-Ng" line from the
parameter file to a new line that starts with "Oh-Cg-Cg-N ". Note the
space after N to ensure that the alignment is preserved.

On Thu, Sep 12, 2013 at 2:10 PM, Lachele Foley <> wrote:
> I believe you might be the first person to try N-linking a sugar with
> an attachment at the 2-position. We are discussing the most
> appropriate resolution. I will respond as soon as I can.
> On Thu, Sep 12, 2013 at 1:31 PM, lara lara <> wrote:
>> dear amber !
>> I am trying to fuse the protein to the glycans in xleap using the GLYCAM_06
>> lib.
>> When I went through the documentation the N -glycosylation site for ASN
>> residue must be changed to label NLN , I did it.
>> I tried to build the carbohydrate from the side chain of the ASN , in the
>> atom ND2 , I am able to build it , but when I saved the parameter file It
>> says the error in Building topology.
>> Building atom parameters.
>> Building bond parameters.
>> Building angle parameters.
>> Building proper torsion parameters.
>> ** No torsion terms for Os-Cg-Cg-N
>> Building improper torsion parameters.
>> old PREP-specified impropers:
>> total 364 improper torsions applied
>> 0 improper torsions in old prep form
>> Building H-Bond parameters.
>> Parameter file was not saved.
>> I feel that the atom type to the atoms should be changed , but i dont know
>> which type is relevant ( the ND2 type is N so that is saying error )
>> how to fix this ?
>> thanks in advance
>> _______________________________________________
>> AMBER mailing list
> --
> :-) Lachele
> Lachele Foley
> Athens, GA USA

:-) Lachele
Lachele Foley
Athens, GA USA
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Received on Fri Sep 13 2013 - 07:30:03 PDT
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