Re: [AMBER] Antechamber on unknown residue

From: David Case <>
Date: Mon, 8 Oct 2018 13:29:41 +0000

On Mon, Oct 08, 2018, Keiran Corbett wrote:

> I am using this tutorial to generate parameters for an unkown residue I
> have
> I downloaded the .cif file from the pdb website
> When I run this command I get this error
> antechamber -fi ccif -i TYS.cif -bk TYS -fo ac -o -c bcc -at gaff
> syntax error near line 2
> Target data block TYS is not in file

I can't reproduce this error. However (using AmberTools18) I get an
expected message:

slater% antechamber -fi ccif -i TYS.cif -bk TYS -fo ac -o -dr no

Welcome to antechamber 18.0: molecular input file processor.

/home/case/amber18/bin/to_be_dispatched/antechamber: Fatal Error!
Residue (TYS) has a type of LINKING.

Antechamber indeed requires a complete molecule (not just a modified
residue, which is a fragment) in order to be used as above.

It seems you can't turn off this message even with "-dr no". Since this
breaks the tutorial, we need to figure out a way to turn off this error
message....(Scott?) As a workaround, just edit your TYS.cif file to
change the chem_comp.type to something like "NON-POLYMER".

Thanks for the report.....dac

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Received on Mon Oct 08 2018 - 06:30:03 PDT
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