AMBER Archive (2008)

Subject: Re: AMBER: (no subject)

From: Junmei Wang (junmwang_at_gmail.com)
Date: Mon Jun 23 2008 - 10:01:39 CDT

Without the pdb file, it is difficult to figure out the problem. Usually the
error is caused by missing hydrogen atoms or the pdb format not being
correctly parsed by antechamber. You may run acdoctor in the latest amber
version or ambertools to find the problem.

Best

Junmei

On Sun, Jun 22, 2008 at 6:46 PM, Daniel B. Kaplan <dkaplan_at_stevens.edu>
wrote:

> I have a chain of benzene rings in a .pdb file. I want to put an atom
> below the chain to simulate a probe. In the .pdb file everything works
> fine; however, when I run the file through antechamber to convert it to
> a .prepin file, the output contains no information about the atom I
> placed in the .pdb file except three coordinates (two of which are nan
> "not a number"). Also, it contains conflicting an X in the column which
> describes how many atoms that atom is connected to. How do I resolve
> this issue.
> Dan
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