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 <daniel.r.roe.gmail.com> 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 <david.case.rutgers.edu>
> 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
