[AMBER] AMBER VS QM energy calculations for dihedrals

From: Palermo Giulia <giulia.palermo.iit.it>
Date: Wed, 28 Apr 2010 16:09:50 +0200

Dear all,
I am checking the energies of amber force field (gaff, parametrized with antechamber and resp charges)
of a ligand for the rigid rotation around a torsion
against HF/DFT energies. My aim is to perform a conformational sampling by means of straigtforward MD.
The complex is a piperidine 1-caboxylic acid phenylamine that is something like

    h h1
     c-c o1
    / \ ||
 h-c c-c - n-......
    \ / h
    h h

When I rigidly (no minimization upon torsion change) rotate the torsion around the Npiperidine - Ccarbonilic - NH - Caromatic dihedral angle
(atom type: n-c-n-ca) I found that, when h1(type 'ha' in gaff) is less than 1.59 angstrom from o1 (type 'o' in gaff ) I obtain a very high energy for the
force field (around 150 kcal/mol) mostly due to wdV terms (calculated by doing a single step in sander). In HF and various DFT for the same configuration
I do not obtain this peak (the barrier for the rotation stays around 6/7 kcal). If I carry out a non rigid torsion scan this effect is not
present anymore. So I am a bit in doubt regarding the force field I'm about to use for this ligand.
My questions are:
1) Should I worry about this effect ?
2) Is there any way to understand if this is an artifact of the force field or of the HF/DFT scheme?
3) Is there anything i can control to avoid this behaviour in the force field (assuming this is something which is worth correcting for the
problem I'm about to study. see above)?

Many thanks in advance


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Received on Wed Apr 28 2010 - 07:30:03 PDT
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