AMBER Archive (2006)

Subject: AMBER: LEaP Warning ... when do NH2-neutral fragment

From: jitrayut jitonnom (
Date: Tue Jun 13 2006 - 13:40:47 CDT

 Dear amber users

I am preparing a file for a ligand at pH11 which there is a little chage in
the N-terminal of alanine (ALA) amino acid. Now, I can do this by using
'set' commands to make NH2-terminal. However, there is a warning in the last
step of LEaP (show below). So, I am not sure that this error can be ignored
or not. Actually, I found that all parameters in the prepin file are ok
and the pdb file (p1_1n_min_OK.pdb) is correct. Therefore, my question is
how to check this error or where is the file that I should be check at first

This is the warning in LEaP :
> check as
Checking 'as'....
Warning: Close contact of 1.792161 angstroms between .R<ALD 1>.A<C 10> and
.R<ALA 2>.A<N 1>
Checking parameters for unit 'as'.
Checking for bond parameters.
Could not find bond parameter for: O - N
Checking for angle parameters.
Could not find angle parameter: O - N - H
Could not find angle parameter: O - N - CT
Could not find angle parameter: C - O - N
There are missing parameters.
check: Warnings: 1
Unit is OK.
> savepdb as p1_1n_min_OK.pdb
Writing pdb file: p1_1n_min_OK.pdb
 Converting C-terminal residue name to PDB format: CARG -> ARG
> quit

Thank you in advance,

Best regards,

Jitrayut Jitonnom, Ph.D.
Computational Simulation,
and Modeling Laboratory (CSML),
Chiang Mai University, Thailand.
Tel: +66(0)6 613 4218

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