AMBER: leap warnings

From: mathew k varghese <>
Date: Mon, 14 Mar 2005 06:34:32 +0000 (GMT)

Dear amber users,

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>
Warning: Close contact of 1.050040 angstroms between
..R<RC 6>.A<H42 21> and .R<WAT 46>.A<H2 2>
Warning: Close contact of 1.964182 angstroms between
..R<RU 8>.A<HO'2 29> and .R<WAT 36>.A<H2 2>
Warning: Close contact of 2.120098 angstroms between
..R<RU 8>.A<H3 21> and .R<RA 11>.A<N1 22>
Warning: Close contact of 1.708330 angstroms between
..R<WAT 33>.A<H1 1> and .R<WAT 38>.A<H2 2>
Warning: Close contact of 2.163305 angstroms between
..R<WAT 43>.A<H2 2> and .R<WAT 50>.A<O 3>
Warning: Close contact of 1.532678 angstroms between
..R<WAT 43>.A<H2 2> and .R<WAT 50>.A<H1 1>
Checking parameters for unit 'ar1'.
Checking for bond parameters.
Checking for angle parameters.
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"?




Mathew K Varghese
Research Scholar
School of Pure and Applied Physics
Kottayam, Kerala



Yahoo! India Matrimony: Find your life partner online
Go to:
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Mon Mar 14 2005 - 06:53:00 PST
Custom Search