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

From: Alfredo Quevedo <>
Date: Fri, 19 Aug 2016 14:49:05 -0300

Thank you Prof. Case for the reply.

As you suggest I tried removing the LINKING string and everythin worked
as expected,

best regards


El 19/08/2016 a las 14:43, David A Case escibió:
> 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
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Prof. Dr. Mario Alfredo Quevedo.-
Laboratorio de Química Medicinal.-
Dpto. de Farmacia - Fac. de Ciencias Químicas.-
Universidad Nacional Córdoba.-
5000 Córdoba, Argentina
TE: +54 351 5353865 Int: 53355
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Received on Fri Aug 19 2016 - 11:00:02 PDT
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