AMBER Archive (2006)
Subject: AMBER: problem with prep file
From: Simon Whitehead (SJW084_at_bham.ac.uk)
Dear amber users,
I am getting a little frustrated trying to create a prep file for leap for my substrate. I have converted a pdb file to prep file. When i check the parameters using parmchk it creates a frcmod file with the unknown bond lengths, angles, dihedrals etc generated. However when i change the atom names in my prep file to match those of my pdb and repeat the parmchk i get several values in the frcmod that require attention, for example,
h1-h1 0.00 0.000 ATTN, need revision
This seems very strange indeed as there are no H-H bonds and the connectivity in the prep file is unchanged.
Has anyone any ideas?