Re: [AMBER] Tutorial B5 - Loading CRO from ccif file

From: David A Case <>
Date: Fri, 19 Aug 2016 13:43:15 -0400

On Fri, Aug 19, 2016, Alfredo Quevedo wrote:

> I am trying to reproduce tutorial B5 ("Simulating the Green Fluorescent
> Protein") and when executing the command:
> $ antechamber -fi ccif -i CRO.cif -bk CRO -fo ac -o -c bcc -at amber
> I am getting "/Residue CRO has a type of LINKING. Quitting/" as output.
> I can see that this behaviour is a consequence of Update.8 on
> antechamber. So my question is: why shouldnt antechamber process the CRO
> unit if it is marked as a linking unit? How can I solve this issue in
> order to safely compute the parameters for this unit?

Oh, my, what a tangled development we have here....I was trying to accomplish
too many things with one piece of code.

Easiest fix for now is to edit the CFO.cif and remove the "LINKING"
part of the _chem_comp.type entry.

I'll try to figure out a more correct fix (extra flag to allow/disallow
LINKING residues? more major refactoring?)

...thanks for the report...dac

AMBER mailing list
Received on Fri Aug 19 2016 - 11:00:02 PDT
Custom Search