AMBER Archive (2005)

Subject: RE: AMBER: Searching for NAD parameter files / Problems with parameter file creation

From: Rhoad, Jonathan S. (rhoadj_at_missouri.edu)
Date: Thu Jun 23 2005 - 10:08:01 CDT

Daniel,

>I also tried to generate parameter files myself using
>antchamber. I mannaged to create a file but if I use it,
>the NAD appears two times in my model since the NAD
>is added a 2nd time as a bunch of heteroatoms.

Without your input files it is impossible to tell for sure, but I will
hazard a guess. If you have the proper Residue name, but the atom names
from your pdb do not EXACTLY match the expected atom names from the .off
it will add all of the atoms that are missing.

Hope this helps.

Jonathan Rhoad
123 Chemistry
Life Sciences Post-doctoral Fellow
Department of Chemistry
University of Missouri-Columbia
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu