AMBER Archive (2005)

Subject: AMBER: leap warnings

From: mathew k varghese (mathew_kvarghese_at_yahoo.co.in)
Date: Mon Mar 14 2005 - 00:34:32 CST

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

===========================================================================

/\/\athew

Mathew K Varghese
Research Scholar
School of Pure and Applied Physics
M.G.University
Kottayam, Kerala
India

email mathew_kvarghese_at_yahoo.co.in

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