RE: AMBER: NAD parameters

From: Ross Walker <>
Date: Mon, 30 Jan 2006 08:34:20 -0800

Dear Alexandra

> +Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
> +---Tried to superimpose torsions for: *-C18-N7-*
> +--- With Sp2 - Sp0
> +--- Sp0 probably means a new atom type is involved
> +--- which needs to be added via addAtomTypes

This message comes about because the hybridisation in Leap is not defined
for these atoms. This information is used by Leap in two places. Firstly
when placing atoms that are missing from the pdb file and secondly when
using Leap's internal minimisation to relax the position of some atoms. It
does not play a part in the prmtop file. Thus if all your atoms are present
in your pdb file you should not have a problem. All of the parameters
required for the prmtop file are explicitly defined in the NAD+ frcmod file.

You could use the addAtomTypes command to explicitly define the
hybridisation of the relevant atoms but this will only serve to remove the
warnings and allow correct missing atom placement an minimisation in Leap.
For most purposes the above warnings can be considered inoccuous.

I should probably modify the Lib file at some point to include the

All the best

|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel: +1 858 784 8889 | EMail:- |
| | PGP Key available on request |

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Received on Mon Jan 30 2006 - 22:08:54 PST
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