Hi!
I'll take a look at the table. It might need updating.
We now use uppercase-lowercase type names, e.g., Cg rather than CG. The various ffs decided this mutually to avoid parms clashes.
:-) Lachele
Dr. B. Lachele Foley
Associate Research Scientist
Complex Carbohydrate Research Center
The University of Georgia
Athens, GA USA
lfoley.uga.edu
http://glycam.org
________________________________________
From: Gerald Monard <Gerald.Monard.univ-lorraine.fr>
Sent: Friday, June 26, 2015 7:42 AM
To: AMBER Developers Mailing List
Subject: Re: [AMBER-Developers] ff14SB strange parameter assignment
Hello,
I don't know if every body is aware of this: there is a web page
(
http://ambermd.org/doc/AtomTypesTableWorkspace.xhtml) that lists all
the atom types that are defined in the different "amber" force fields.
Thanks to "git blame", the author is Daniel from a
AtomTypesTableWorkspace.lyx file (available in the doc/ directory of the
amber master tree) by Lachele. Thanks to both of them for providing this
useful information :-).
From that file, it seems that CG is already defined in GLYCAM...
Gerald.
P.S.: It dates from 2012 and does not include ff14SB, but there should
be some way to automate the process.
On 06/26/2015 04:13 AM, James Maier wrote:
> Thanks, Jason.
>
> I have deleted the line in the master branch. We can safely move on :-)
>
> Best,
>
> James
>
> On Wed, Jun 24, 2015 at 11:52 AM, Jason Swails <jason.swails.gmail.com>
> wrote:
>
>> Hi everyone (although probably James in particular),
>>
>> Someone recently brought up a potential concern within frcmod.ff14SB. In
>> particular, there is a line:
>>
>> HP-CX-CG 50.0 109.50 changed based on NMA nmodes (was CT-CT-HP)
>>
>> that defines an angle parameter involving atom type CG. However, atom type
>> CG doesn't exist in the ff14SB force field (it's not defined in parm10.dat
>> or anywhere else). As-is, this line is a no-op and has no effect on the
>> force field at all. But could this be a typo? Perhaps it was *intended*
>> that CG be replaced with a different atom type? Or can we just delete this
>> line and move on?
>>
>> Thanks,
>> Jason
>>
>> --
>> Jason M. Swails
>> BioMaPS,
>> Rutgers University
>> Postdoctoral Researcher
>> _______________________________________________
>> AMBER-Developers mailing list
>> AMBER-Developers.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber-developers
>>
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>
--
____________________________________________________________________________
Prof. Gerald MONARD
SRSMC, Université de Lorraine, CNRS
Boulevard des Aiguillettes B.P. 70239
F-54506 Vandoeuvre-les-Nancy, FRANCE
e-mail : Gerald.Monard.univ-lorraine.fr
tel. : +33 (0)383.684.381
fax : +33 (0)383.684.371
web : http://www.monard.info
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Received on Fri Jun 26 2015 - 10:30:02 PDT
