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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Received on Thu Jan 17 2013 - 00:00:02 PST
