Re: [AMBER] RNA with ligand - a follow-up ANTECHAMBER question

From: David A Case <>
Date: Wed, 25 Oct 2017 22:35:50 -0400

On Wed, Oct 25, 2017, Kasprzak, Wojciech (NIH/NCI) [C] wrote:
> The ligand is positively charged (+1), and the (Amber 14) antechamber call I used was as follows:
> > antechamber -i LIG.pdb -fi pdb -o LIG-A14ante-bcc.mol2 -fi mol2 -nc 1 -m 2 -s 2

I don't know what you ligand really is, but you should check that it really
has an odd number of electrons. The antehcamber scheme will only work for
closed-shell molecules. If you really have a stable radical, constructing
a force field for it will almost certainly involve a lot of hand-work. But
Arzoxifene itself has an even number of electrons, and *very* few organic
drug-like molecules are radicals.

> Chimera GUI, on the other hand, issues the following command:
> > antechamber -ek qm_theory='AM1', -i LIG.mol2 -fi mol2 -o LIG-ante.mol2
> > -fo mol2 -c bcc -nc 1 -j 5 -s 2
> Thus the multiplicity of 1 is assumed (default) and -j 5 - atom and part
> bond type.

Something odd is going on here, if the same +1 charge can yield structures
with both even and odd numbers of electrons. I don't think anyone on the list
will be able to resolve this without more information.


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Received on Wed Oct 25 2017 - 20:00:01 PDT
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