Dear Amber !
Thank you for the reply , I will check this and try .
On Fri, Sep 13, 2013 at 10:09 AM, Karl N. Kirschner <
kkirsch.scai.fraunhofer.de> wrote:
> 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,
> Karl
>
> ----- Original Message -----
> From: "Lachele Foley" <lf.list.gmail.com>
> To: "AMBER Mailing List" <amber.ambermd.org>
> 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
> precedent.
>
> 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 <lf.list.gmail.com> 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 <lara.4884.gmail.com> 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
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> >
> > --
> > :-) Lachele
> > Lachele Foley
> > CCRC/UGA
> > Athens, GA USA
>
>
>
> --
> :-) Lachele
> Lachele Foley
> CCRC/UGA
> Athens, GA USA
>
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Received on Mon Sep 16 2013 - 08:00:05 PDT
