Re: [AMBER] Query regarding parmchk

From: case <>
Date: Wed, 26 Jan 2011 11:53:24 -0500

On Wed, Jan 26, 2011, wrote:

> Thanks for advice. Creating the mol2 file using antechamber helped so
> I got the frcmod files.So in the next step I wanted do generate the
> prmtop and inpcrd files and get the following error:

First, you need to manually examine the mol2 and frcmod files that were
created. We don't have any idea how you created these files, but they
can you help a lot in debugging.
> WARNING: There is a bond of 4.899159 angstroms between:
> ------- .R<ATU 720>.A<C10 17> and .R<ATU 720>.A<C11 20>

So, is there supposed to be a bond between C10 and C11? Is the distance
in the mol2 file really 4.9 Ang? This suggests that the pdb file you used as
input to antechamber was badly flawed (check that). If the input geometry
is not reasonable, antechamber will fail.

> WARNING: The unperturbed charge of the unit: 15.002000 is not zero.

This sounds odd: is the charge supposed to be 15?

> FATAL: Atom .R<ATU 720>.A<O22 34> does not have a type.

Look in the mol2 or lib file: is there a type for O22?

Based on very limited evidence, it looks like antechamber did not do what you
expected it to do.


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Received on Wed Jan 26 2011 - 09:00:05 PST
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