AMBER Archive (2006)

Subject: Re: AMBER: xleap not recognizing residue

From: David A. Case (
Date: Sun May 07 2006 - 20:50:06 CDT

On Sun, May 07, 2006, Kenley Barrett wrote:

> I just created a new library file for a methylated histidine. Initially
> everything appeared to be fine (XLeap read in the pdb file containing the
> methylated histidine without complaining), but then when I tried to set the
> connect0 and connect1 atoms XLeap told me that "HMH", my residue name, was
> not a residue:
Here is the problem, in your lib file:

> !entry.HMH.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
> "" 1 27 1 "?" 0

The first blank string should be "HMH", not a blank. This is why you are
getting a blank residue id after you load the pdb file. (You can use the
"desc" command after you load the pdb to see what it going on.)

How (in detail) did you create the lib (aka "off") file? We need to figure
out if something was supposed to be inserting this string and was not.
But if you manually fix the lib file, you should be able to get further.

...good luck...dac

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