Re: [AMBER] wrong ligand geometry

From: David A Case <>
Date: Sun, 27 Aug 2017 08:40:51 -0400

On Sat, Aug 26, 2017, Thomas Evangelidis wrote:
> I need some advice about force field modification. I have a series of
> ligands that have this imino-hydantoin moiety in common. The frcmod.ligand
> file generated with parmchk has only IMPROPER angle definitions (is this
> normal?).

Please use parmchk2, not parmchk. [It was a mistake to even have parmchk
built anymore. The notion was that some people might want/need to re-run
old results. But the danger of using it (parmchk) by mistake is too great.]

The frcmod file by default will contain only paramters that are *not* in
gaff.dat or gaff2.dat. It is often helpful to use the "-a" flag to have
parmchk2 print out all the parameters, so you have them in one place.

> Particularly, the hn proton shown in the picture below is out of the place
> of the aromatic imino-hydantoin ring. In the IMPROPER section, there is a
> dihedral angle definition for that (c2-c3-nh-hn), therefore I wonder why it
> does not remain on the aromatic plane during the MD simulation. What
> modifications could I make in the frcmod file in order to maintain the
> aromaticity of imino-hydantoin moiety?

This may be more a question of atom typing than parameters (not sure). The
nh type is an "amine N connected to one or more aromatic rings", and it is
common for hydrogens in such circumstances to be (somewhat) out of plane. But
it is likely that you know more about these particular geometric preferences
than I do. Have you done a search for other molecular mechanics studies
of systems like this?


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Received on Sun Aug 27 2017 - 06:00:04 PDT
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