Re: [AMBER] non standard Alanine

From: FyD <>
Date: Fri, 04 Mar 2011 16:50:50 +0100

Dear Massimiliano,

> I would need to model a 8 residues long peptide, whose first (N-term) residue
> is the D-isomer of the Alanine and whose C-terminus is capped with
> -NH2 group.
> I would like ask you the following questions:
> - Is there any residue name recognized by tleap that I could use for
> the capping group -NH2?

You could create a new -NH2 capping group using the CH3CONH2 molecule
or any similar model...

If you use R.E.D. III.4 or R.E.D. Server (it is down this week-end),
you create a P2N file, add the INTRA-MCC keyword for defining the
intra-molecular charge constraint (set to zero) applied during the
fitting step for the CH3CO capping group.
The same principle could be followed for any capping group using a
single intra-molecular charge constraint.

You should introduce a small error when applying this intra-molecular
charge constraint; however, the idea is only to create a capping group
compatible with other residues...

> - How can I change the improper torsion parameters for the D-Ala
> residue in order to keep it as D-isomer?

If your amino-acid is L or D in the PDB file it should be recognized
by a FF library (L-residue, by default) if the residue name/atom names
in the FF library match these in the PDB file. Just check the S/R
chirality of the CA centers in the input PDB file (& use NMR
restraints for CA during MD simulations/geometry optimizations_?).

regards, Francois

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Received on Fri Mar 04 2011 - 08:00:02 PST
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