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

From: Jag Silwal <>
Date: Fri, 19 Jun 2020 17:55:42 -0400

Dan and all,

Thank you for your response.
For a novice like myself, could you please send me the file with the EOL,
as an example, so that I can proceed with the ambpdb?

On Fri, Jun 19, 2020 at 5:30 PM Daniel Roe <> wrote:

> Hi,
> 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
> file.
> > 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!).
> -Dan
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Received on Fri Jun 19 2020 - 15:00:04 PDT
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