AMBER Archive (2006)

Subject: Re: AMBER: problem with prep file

From: David A. Case (
Date: Wed May 10 2006 - 11:12:59 CDT

On Wed, May 10, 2006, Simon Whitehead wrote:
> 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.

I don't think we can help without seeing what the differences between the
"working" and the "non-working" prep file are. It is also not clear why
the original prep file (which was prepared from a pdb file) doesn't have the
same atom names as the pdb file. Antechamber takes its names from the input
pdb file, so something funny must be going on.

I don't think it's possible for anyone to help without more information.
Basically, all you have said so far is "parmchk gives a bad result".


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