AMBER Archive (2005)

Subject: RE: AMBER: leap warnings

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Mon Mar 14 2005 - 00:56:17 CST

Dear Mathew,

> When I load a rna pdb file which contains
> crystallographic waters to leap and check the unit it
> issues a number of warnings.
> ========================================================
> Checking 'ar1'....
> WARNING: The unperturbed charge of the unit:
> -17.000000 is not zero.
> FATAL: Atom .R<CA 20>.A<CA 1> does not have a type.
> FATAL: Atom .R<CA 21>.A<CA 1> does not have a type.
> Warning: Close contact of 2.159251 angstroms between
> .R<RA 4>.A<N1 22> and .R<RU 15>.A<H3 21>
> Warning: Close contact of 1.987463 angstroms between
> .R<RC 6>.A<O2 24> and .R<RG 13>.A<H21 24>
.
.
.
> check: Errors: 2 Warnings: 9
> =======================================================
> I think I have to create atom types for the calcium
> ions and should nutralise the unit with addions
> command. But what should I do about the other
> warnings, "close contact"?

You are correct, you will need to define the parameters for the calcium
ions. Although I think calcium may be available in the default libraries.
Check ions.lib in the leap dat directory. Is it being loaded? Try loadoff
ions.lib if it isn't. This is assuming you wish to treat them as
non-covalently bound ions. Otherwise you will have to bind them to something
and provide bond, angle and dihedral data.

As for neutralising your unit, since you will, I guess, be doing an explicit
solvent simulation with PME you will need a neutral system so should
probably neutralise it with 17 Na+ ions.

As for the close contacts these are just warnings. The close contacts are
just warning you that if you start your system off with Molecular Dynamics
straight from the get go it is likely to explode. With explicit solvent
simulations it is nearly always necessary to minimise your system before
starting MD so you can safely ignore these warnings since the minimisation
should fix up any close contacts. You really only need to worry about close
contact warnings when the value is below an angstrom or so... Perhaps we
should change the threshold for the warning...

I hope this helps.
All the best
Ross

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