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GLYCAM-L  February 2020

GLYCAM-L February 2020

Subject:

Re: Amber tleap: Fatal error "Atom does not have file type" -reg

From:

Lachele Foley <[log in to unmask]>

Reply-To:

Users of GLYCAM & GLYCAM-Web <[log in to unmask]>

Date:

Tue, 11 Feb 2020 11:45:57 -0500

Content-Type:

text/plain

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Parts/Attachments

text/plain (117 lines)

I think you just need to supply an output file name and output file type.

antechamber -fi ac -i STG.ac -c wc -cf STG.crg  -fo FILETYPE -o FILENAME

On Mon, Feb 10, 2020 at 2:46 PM Alejandro Cagnoni
<[log in to unmask]> wrote:
>
> Hi
>
> How are you? I'd like to ask you for some help with an antechamber issue.
>
> I am trying to parametrize a structure but I'm having some trouble. I attach here the script. There seems to be some problem with the output file format.
>
> alejandrocagnoni@julia:~/Dropbox/IBYME/colaboraciones/Lisandro Otero/paper 2019/MD$ antechamber -fi ac -i STG.ac -c wc -cf STG.crg
>
> Welcome to antechamber 17.3: molecular input file processor.
>
> acdoctor mode is on: check and diagnosis problems in the input file.
> -- Check Format for ac File --
>    Status: pass
> -- Check Unusual Elements --
>    Status: pass
> -- Check Open Valences --
>    Status: pass
> -- Check Geometry --
>       for those bonded
>       for those not bonded
>    Status: pass
> -- Check Weird Bonds --
>    Status: pass
> -- Check Number of Units --
>    Status: pass
> acdoctor mode has completed checking the input file.
>
> /home/alejandrocagnoni/Documentos/amber18/bin/to_be_dispatched/antechamber: Fatal Error!
> Unknown output file format ().
>
> Could you please help me?
>
> Thank you very much
>
> Best regards
>
> Alejandro
>
>
> --
> Dr. Alejandro J. Cagnoni
>
> Instituto de Biología y Medicina Experimental
> Consejo Nacional de Investigaciones Científicas y Técnicas
> Buenos Aires (1425), Argentina
> (011)47832869. int. 204
>
> On Fri, Aug 23, 2019 at 12:54 PM R A Jeyaram 16PHD0482 <[log in to unmask]> wrote:
>>
>> Thank you very much for your valuable suggestions mam.
>>
>> On Fri 23 Aug, 2019, 9:19 PM Lachele Foley, <[log in to unmask]> wrote:
>>>
>>> I haven't built force field params in a while, so others might have
>>> better (more recent) information than what I'm about to say.  You will
>>> need to use GAFF for the parameters except for the partial charges.
>>> You will need to translate the parameters for the atom types in the
>>> rest of the monosaccharide.  It will probably be best to generate a
>>> frcmod file containing the gaff params you need that bridge the type
>>> naming systems.  After that, you will need to make a best-guess
>>> initial charge set and, based on that, compute a better,
>>> ensemble-averaged set of partial charges for the residue.  The latter
>>> requires an MD simulation and a representative sample of quantum
>>> calculations to be run on geometries from the simulation.
>>>
>>> If what I just said makes no sense to you, then it will take a lot of
>>> work for you because you will have to learn all those things.  I don't
>>> know if any of the folks in our lab have time to spare to help you
>>> with this.  I don't know if we have time even to do any training right
>>> now, but might in the not too distant future.
>>>
>>> On Wed, Jun 26, 2019 at 1:44 AM R A Jeyaram 16PHD0482
>>> <[log in to unmask]> wrote:
>>> >
>>> > Dear Glycam Users,
>>> >
>>> >                  I am using Amber16 package and glycam force filed for MD simulation. My ligand file containing sialic acid and I substitute fluorine atom into O4 position of sialic acid. During the preparation of topology and parameter files via tleap module of Amber, I have the Fatal error as "Atom does not have file type" for fluorine atom. How can I parameterize fluorine atom.
>>> >                                         Thanks in Advance
>>> > with regards
>>> > R. A. Jeyaram
>>> > Research Scholar
>>> > School of Advanced Sciences
>>> > Vellore Institute of Technology
>>> > Tamil Nadu, India.
>>>
>>>
>>>
>>> --
>>> :-) Lachele
>>> Lachele Foley
>>> CCRC/UGA
>>> Athens, GA USA
>
>
>
> --
> Dr. Alejandro J. Cagnoni
>
> Instituto de Biología y Medicina Experimental
> Consejo Nacional de Investigaciones Científicas y Técnicas
> Buenos Aires (1425), Argentina
> (011)47832869. int. 204



-- 
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA

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