Re: [AMBER] ATP and ADP-Pi simulations

From: Joseph Baker <bakerj.tcnj.edu>
Date: Wed, 4 Mar 2015 00:36:07 -0500

Dear Francois,

Thanks for the links. I took a look at the RED DB info, and it is not clear
to me how to manipulate what is in that database to obtain an inorganic
hydrogen phosphate and inorganic dihydrogen phosphate. Is that possible
using what is in the F-90 project?

Kind regards,
Joe

--
Joseph Baker, PhD
Assistant Professor
Department of Chemistry
C101 Science Complex
The College of New Jersey
Ewing, NJ 08628
Phone: (609) 771-3173
Web: http://bakerj.pages.tcnj.edu/
<https://sites.google.com/site/bakercompchemlab/>
On Tue, Mar 3, 2015 at 4:28 AM, FyD <fyd.q4md-forcefieldtools.org> wrote:
> Dear Joseph,
>
> See also the F-90 REDDB project:
> http://q4md-forcefieldtools.org/REDDB/projects/F-90/
> http://q4md-forcefieldtools.org/REDDB/projects/F-90/script1.ff
>
> On the top of the FF parameters you can always add your own set of FF
> paramters.
>
> R.E.D. Server/R.E.D. IV are outdated!
> Please use instead: R.E.D. Server Dev./PyRED at
> http://q4md-forcefieldtools.org/REDServer-Development/
>
> See http://q4md-forcefieldtools.org/REDServer/images/AnteRED-RED.gif
>   vs
> http://q4md-forcefieldtools.org/REDServer-Development/images/PyRED.gif
>
> PyRED generate a whole force field i.e. not only atomic charges.
>
> See the tutorial:
> http://q4md-forcefieldtools.org/Tutorial/Tutorial-4.php
>    & in particular the last ones:
> http://q4md-forcefieldtools.org/Tutorial/Tutorial-4-demo1.pdf
> http://q4md-forcefieldtools.org/Tutorial/Tutorial-4-demo5.pdf
> where you can provide your own atom types (or correct theses
> automatically generated) and mandatory/missing force field parameters...
>
> the mol3 file format is the default file format for FF libraries:
> http://q4md-forcefieldtools.org/Tutorial/leap-mol3.php
> (it is advantageous for molecular fragments)
>
> regards, Francois
>
>
>
> > I see that the Carlson group has some ADP and ATP parameters that have
> been
> > developed for use with ff99SB. However, from my understanding, ff12SB or
> > ff14SB are now recommended for protein simulation due to some
> improvements
> > in how they treat protein secondary structure. Is anybody aware of
> whether
> > the Carlson ADP/ATP parameters have been vetted against ff12SB or ff14SB,
> > or if one should expect the modifications that went into those
> force-fields
> > to break anything badly if they are used with the Carlson ADP/ATP
> > parameters? I'm curious because I saw a recent (2013) nice paper from the
> > Hummer group on F1-ATPase where they still used the combination of ff99SB
> > with these Carlson parameters.
> >
> > Also, does anyone know if there are any parameters for HPO42- or H2PO4-
> > floating around out there that have been tested with Carlson ADP +
> > ff99SB/ff12SB/ff14SB? If not then I'll go with the antechamber + RED
> server
> > route.
>
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber

Received on Tue Mar 03 2015 - 22:00:02 PST