AMBER Archive (2009)

Subject: [AMBER] Tleap input error, atom not found in residue template

From: Brothers, Michael Charles (mcbroth_at_sandia.gov)
Date: Mon Jul 06 2009 - 20:25:00 CDT

Amber Users,

I am having a strange issue where all but one atom in my pdb file is being recognized. I've tried ff99sb and ff03 forcefields so far. Upon loading this into tleap, it is adding three hydrogens to places there were lone pairs (I'm assuming from adding hydrogens to nitrogen lone pairs). It also spits back a message that one atom isn't found in the residue template. This is causing an error in the output of the prmtop file when I use saveamberparm. I believe this is an issue with the carboxy terminus, but I have tried multiple variations and have checked other input files and have had little luck.

Any idea how to fix the nomenclature to avoid the error?

Thanks!

Mike


  • application/octet-stream attachment: AAA.pdb

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