Dear Francois
Thank you. My molecule is composed a direct binding of sugar at C1 and the lysine (NZ). The nitrogen atom has a single hydrogen atom. Please, I have still more questions, should I copy CT-N3- CT in frcmod as text. and should I apply ff99SB and Glycam_06h together or only ff99SB at leap. I attached my file as FUL.mol2.
Regards,
John
> Date: Thu, 17 Jan 2013 08:57:27 +0100
> From: fyd.q4md-forcefieldtools.org
> To: amber.ambermd.org
> Subject: Re: [AMBER] A link atoms between protein and sugar!
>
> Dear John,
>
> > I built a protein-sugar complex. The lysine residue (NZ atom) is
> > involved in the binding to sugar (C1 atom). I separated lysine-sugar
> > residue to generate a library for this complex. I used R.E.D server
> > to assign its charges and get a FUL.mol2 file. The problem is, I
> > can do not no how can I parameterize the angle CT-N3-Cg, a bond
> > between a GLYCAM_06h
> > atom type and an amber atom type. Please, can I get any suggestions.
>
> The atom type for NZ of LYS is N3 (& the atom type of HE (connected to
> carbon CE) is HP) because NZ is an ammmonium group.
>
> What is this connection? is it a peptide bond?
>
> -> if yes, you end up with:
> H1 O HC
> Lys-CT-N-C-Cg-Cg-Sugar
> H1 H HC
> or
> H1 O H1
> Lys-CT-N-C-Cg-OS-Sugar
> H1 H H1
>
> -> if no, I guess you need up with a secondary amine (or send a
> drawing of this connection):
> H1 H1
> Lys-CT-NT-Cg-Cg-Sugar
> H1 H H1
> or
> H1 H2
> Lys-CT-NT-Cg-OS/Os-Sugar
> H1 H H2
>
> if you only need CT-N3-Cg; this the same than CT-N3-CT (copy it in a
> frcmod file); but I do not think you should use N3; if you have an
> amine (& not an ammonium) you should use NT (& consequently H1 for HE
> connected to CE).
> see $AMBERHOME/data/leap/parm/parm99.dat
> N3 14.01 0.530 sp3 N for charged amino groups (Lys, etc)
> NT 14.01 0.530 sp3 N for amino groups amino groups
> -> There are errors in many Amber force field topology databases and
> confusion between N3 & NT.
>
> I think once again here that using a black box strategy to assign atom
> types is not a good idea; better understanding what you do...
>
> regards, Francois
>
> PS Please carefully check those new atom types in this GLYCAM...
> h?i?z? version; I have no idea what they mean... I guess CG became Cg
> & I guess H1 remains H1...
>
>
>
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- application/octet-stream attachment: FUL.mol2
Received on Thu Jan 17 2013 - 01:00:02 PST
