Re: [AMBER] CPPTRAJ

From: Jason Swails <jason.swails.gmail.com>
Date: Mon, 25 Jul 2016 11:10:08 -0400

On Thu, Jul 21, 2016 at 6:30 AM, Anna Cebrian Prats <Anna.Cebrian.uab.cat>
wrote:

> Good morning
>
>
> I have used cpptraj to check the topology and the coordinates looks a like
> in a pdb
>
>
> and at the beginning of the process with this command : cpptraj
> 3hs5-Fe-O-ph.top
>
>
> I have obtained this error. What does it means? My topology is created
> wrong?
>
>
> How can I solved? I already check in the manual and with a tutorial and
> suggest that the problem is with the atom order. However, I have been
> renumbered by the pdb4amber. Also can be that the bond is not defined but
> the frcmod file contains such information
>

‚ÄčThis is a well-known bug in tleap that does not result in the correct atom
ordering for systems with cross-linked molecules in some instances.

You can use the "fixatomorder" command in cpptraj to fix your topology file
and trajectory files.

HTH,
Jason


-- 
Jason M. Swails
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Received on Mon Jul 25 2016 - 08:30:03 PDT
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