AMBER Archive (2006)

Subject: AMBER: chirality.c error in xleap

From: Kenley Barrett (
Date: Fri Mar 31 2006 - 16:43:33 CST

Dear AMBER users,

I have created a library file for a methylated histidine which initially
appeared to be functional (I can read it into xleap and type "edit" for the
name of the residue and everything looks alright). However, as soon as I try
to read in a pdb file which requires the use of this library file, xleap
crashes with the following error:

[kbarrett_at_anatase test]$ xleap
-I: Adding /opt/local/amber8/dat/leap/prep to search path.
-I: Adding /opt/local/amber8/dat/leap/lib to search path.
-I: Adding /opt/local/amber8/dat/leap/parm to search path.
-I: Adding /opt/local/amber8/dat/leap/cmd to search path.
-s: Ignoring startup file: leaprc
-f: Source
!FATAL ERROR----------------------------------------
!FATAL: In file [chirality.c], line 121
!FATAL: Message: Atom N14 is not in the first list

I tried changing the name of "N14" thinking that perhaps it was just an
objection to that atom name, but it crashed again with the same message
(except that "N14 is not in the first list" was changed to ""new atom name"
is not in the first list". I tried looking in AMBERHOME for the
chirality.cfile but I didn't manage to find it.

Has anyone else received an error like this when using a new library file? I
would very much appreciate any suggestions on how I should fix this.

Thank you in advance for your advice.


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