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

From: David A Case <>
Date: Fri, 19 Jun 2020 16:41:21 -0400

On Fri, Jun 19, 2020, Jag Silwal wrote:
>I used "ambpdb -p -c act2.crd > h++.pdb" and "ambpdb -p
><act2.crd> h++.pdb" and I got following errors for both.
>Error: Reading format FLAG 'IPOL'
>Error reading topology file ''

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
message. If you remove the last three lines of the prmtop file, things
should be OK.

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.

(for Dan: sometimes, cpptraj will just complain but soldier on if it
finds unknown FLAGs; sometimes it seems to stop; sometimes it seems to
work but ends up with corrupted data. I don't understand the innards of
how cpptraj parses prmtops. Fortran codes like sander/pmemd always use
nxtsec(), looking for a particular named flag; in this way, they never
even see sections with unknown flags, which is great, since extended
prmtops with extra info is a nice feature to have. So it seems that
ambpdb ought to be made to work here.)

>I can not even process any of my older files that I have successfully
>processed using a similar way before. Could it be due to any software
>updates that I am not aware of?

Note that "ambpdb" used to be a fortran program with similar inputs,
whereas now it is a offshoot of cpptraj. So if you older experience was
some time ago, you might have actually been running a different program.
But this is just a guess.


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Received on Fri Jun 19 2020 - 14:00:02 PDT
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