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

From: Alessandro Contini <>
Date: Wed, 17 Jun 2020 15:50:14 +0200

Hi Jag,
first check that "act2-top.txt" actually is the topology file and act2-crd.txt are coordinates. Then, it looks like you are using the "-p" flag on the coordinate and the "-c" flag on the topology. Finally, I suggest you to rename the files as act2-crd.txt->act2.crd and act2-top.txt -> act2.prmtop (just to avoid possible "human" errors while processing the files).



Il 17/06/20 15:39, Jag Silwal <> ha scritto:
> Dear all,
> I was simply trying to combine the coordinate and topology file that I
> obtained front eh H++ server using the following commands and I have been
> getting the following errors for every protein I processed recently.
> I have used both of these commands:
> ambpdb -p act2-crd.txt -c act2-top.txt > jpt.pdb
> and
> ambpdb -p act2-crd.txt <act2-top.txt> jpt.pdb
> Both times I am getting following error message:
> "Error: Could not determine format of topology 'act2-crd.txt'
> It used to always work for me before and it might be a simple fix I am not
> aware of. I would greatly appreciate it if anyone in the community could
> throw quick tips on this.
> I have attached the crd and top file here.
> Thank you
> _______________________________________________
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Prof. Alessandro Contini, PhD
DISFARM - Sezione di Chimica Generale e Organica "Alessandro Marchesini"
Università degli Studi di Milano
Via Venezian, 21 20133 Milano
Tel. +390250314480 Fax. +390250314476
skype alessandrocontini</signatureafterquotedtext>
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Received on Wed Jun 17 2020 - 07:00:05 PDT
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