Re: [AMBER] addAtomType problem

From: David A Case <>
Date: Sat, 2 Jul 2016 08:55:16 -0400

On Thu, Jun 30, 2016, Lea Natalia Toledo Carvajal wrote:

> I try to incorporate two new atom types to the ff of Amber (Cu+2 and
> Omu2) as David suggest , but the problem for to recognise their
> associated parameters is unresolved.

To debug, you need to start slowly, with test cases: add a single new atom
type, building up the frcmod file one step at a time, and making sure that
each step works.

> addAtomTypes{{"Cu+2""Cu""sp3"}{"Omu2""O""sp2"}}

You should certainly add spaces above, ...{"Cu2+" "Cu" "sp3"}.... But see
also below, since this the Cu2+ is a standard atom type.

> Could not find angle parameter: Cu+2 - Omu2 - Omu2

I think(!) this is because you have spaces in the Angle section of the frcmod

> For atom: .R<MOL 341>.A<CUP 1> Could not find vdW (or other)
> parameters for type: Cu+2

You are not adding libraries for metal ions. In AmberTools16, you need
to source leaprc.water.<type>, where <type> is the water model you want.
See the "Ions" section of the Reference Manual for more info.


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Received on Sat Jul 02 2016 - 06:00:04 PDT
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