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GLYCAM-L  August 2019

GLYCAM-L August 2019

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:

Fri, 23 Aug 2019 11:49:07 -0400

Content-Type:

text/plain

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Parts/Attachments

text/plain (39 lines)

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

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