Re: [AMBER] Fwd: Error: Could not determine format of topology

From: Daniel Roe <>
Date: Fri, 19 Jun 2020 17:29:58 -0400


The actual problem here is the topology file has no EOL; cpptraj
attempts to read the IPOL section and gets fewer bytes than expected,
and so returns the error. I opened the file in a text editor, added
the EOL and voila, it works.

On Fri, Jun 19, 2020 at 4:41 PM David A Case <> wrote:
> As the message says, your prmtop file has an FLAG IPOL section (at the
> very end). This is not a known flag, and cpptraj/ambpdb gives the above

This is actually a known flag, although I think it may be deprecated.
Cpptraj will read it as long as there are no other problems with the

> You need to figure out how the prmtop file was created in the first
> place: if it was from the H++ server, you might try contacting them to
> see if they can help.

I second this. If they are writing files with no EOL that's probably
not the intended behavior.

> (for Dan: sometimes, cpptraj will just complain but soldier on if it
> finds unknown FLAGs; sometimes it seems to stop; sometimes it seems to

It should always be fine as long as the FLAGs it expects are there
(like atom names, residue indices, etc). Unknown flags should be fine.
If you have an example where this is not the case please let me know
(and/or open up an issue on GitHub!).


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Received on Fri Jun 19 2020 - 15:00:03 PDT
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