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

From: David A Case <>
Date: Mon, 22 Jun 2020 21:27:32 -0400

On Mon, Jun 22, 2020, Jag Silwal wrote:
>Thank you for the file. This time, I tried both ways using the corrected
>file you sent me. Now I am getting error messages as follows:
>*ambpdb -p <act2.crd> h++.pdb*

The file you attached, called "act2.crd" is actually a prmtop file, not a
coordinate file of any description. I think you are still having file
naming problems-- the actual content of the files doesn't match the
names you are giving them.

For a formatted file, you can just type "head act2.crd" to see what sort
of file it is.

However, the topology file now has dos line endings, which is probably
OK, but it is missing the "0" that was present in the intial file (that
had the missing EOL. Either add the 0 back in, or remove everything
from the line "%FLAG IPOL" to the end of the file, using a text editor.

And do yourself a favor, and don't name a topology file "act2.crd".
It's technically legal (since the file extension is up to you), but
will almost inevitably lead to errors like the one reported above.


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Received on Mon Jun 22 2020 - 18:30:03 PDT
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