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

From: Jag Silwal <>
Date: Fri, 19 Jun 2020 10:07:10 -0400

Hi Dave,

Thank you for your response.

I tried based on your suggestion and I am still getting error. I have
attached the .crd and .top files here (my attachment to the previous reply
was somehow too big and it didn't go through). Could you please see if you
spot any errors on this file? I simply copied the output files from H++ and
renamed them.

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 ''

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?

Thank you again for your response.


On Wed, Jun 17, 2020 at 3:12 PM David A Case <> wrote:

> On Wed, Jun 17, 2020, Jag Silwal wrote:
> >
> >ambpdb -p act2-crd.txt -c act2-top.txt > jpt.pdb
> From the file names, it looks like you have things backwards: you appear
> to be giving the coordinates (act2-crd.txt) with the "-p" flag and
> the topology (act2-top.txt) with the "-c" flag.
> Try swapping the file names.
> ....dac
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Received on Fri Jun 19 2020 - 07:30:03 PDT
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