Re: [AMBER] ATP and ADP-Pi simulations

From: FyD <fyd.q4md-forcefieldtools.org>
Date: Tue, 03 Mar 2015 10:28:50 +0100

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R.E.D. Server/R.E.D. IV are outdated!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.




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Received on Tue Mar 03 2015 - 01:30:03 PST