AMBER Archive (2006)

Subject: AMBER: problem with prep file

From: Simon Whitehead (
Date: Wed May 10 2006 - 05:52:32 CDT

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
ha-hn 0.00 0.000 ATTN, need revision
hc-hc 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?


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