[AMBER] Antechamber error when attempting Tutorial B5

From: David Wright <david.wright.kuano.ai>
Date: Wed, 23 Jun 2021 16:41:22 +0100


I am trying to run through the tutorial for Simulating the Green
Fluorescent Protein from http://ambermd.org/tutorials/basic/tutorial5/

I am using Ambertools 21 installed via conda.

When I get to section 2 and run the command (using the CRO.cif file
downloaded from the tutorial page):

$ antechamber -fi ccif -i CRO.cif -bk CRO -fo ac -o cro.ac -c bcc -at amber

I get the following error:

The atom type is set to amber; the options available to the -at flag are
    gaff, gaff2, amber, bcc, and sybyl.
/home/dave/anaconda3/envs/kuano/bin/wrapped_progs/antechamber: Fatal Error!
Residue (CRO) has a type of LINKING.

The first part of this seems to be a warning as I get it with other
files that go on to be processed correctly. Could anyone suggest what is
going wrong here?


Dave Wright
CTO & Co-Founder
AMBER mailing list
Received on Wed Jun 23 2021 - 09:00:02 PDT
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