I chose the AMBER ATP for OPLS as I wanted to simulate my system with
two different all-atom forcefields and knew that I could use AMBER in
GROMACS with these published parameters (through use of the ffamber
ports). The only other all-atom forcefield in GROMACS at that time was
OPLS and rather
Dear Tom:
Thanks for your suggestion. You are absolutely right on doing more
testings. I simply haven't figure out what the appropriate test is
yet. Could you be more specific about "these parameters perform just
as well as"? What kind of test did you do?
Also, is there a reason why you c
Well I would suggest you should do some very careful testing to validate
the combination of CHARMM charges and one dihedral with the rest of the
parameters from OPLS. It is not very common (or generally wise) to mix
and match parameters from different forcefields, see:
http://www.gromacs.org/i
Hi,
I recently made up a topology for ADP. You can probably modify it to
ATP easily.
I used native OPLS atom types based on the DNA parameters (http://rnp-group.genebee.msu.su/3d/ff.htm
). The charges are copied from CHARMM27. Also, there is one dihedral
angle missing, again, copied from CHA
Sorry realised I posted the amber ATP link wrong, it is without the ) at
the end:
http://www.pharmacy.manchester.ac.uk/bryce/amber
Tom
--On Thursday, February 26, 2009 17:15:22 + TJ Piggot
wrote:
Some of these charges look a bit suspect to me (eg the charge on the
gamma phosphate). If
Some of these charges look a bit suspect to me (eg the charge on the gamma
phosphate). If you do not need to use OPLS then there is ATP included in
the (united atom) gromos forcefields (see the top folder) and also ATP
parameters available for the (all atom) Amber forcefields (see
http://www.ph
On Wednesday, February 25, 2009 12:06:20 AM, Lucio Ricardo Montero Valenzuela
wrote:
> Does anybody have the topology files for ATP and/or ADP for the OPLS-AA
> forcefield?. If not, how can I parameterize this molecules?.
> Best regards.
>Lucio Montero.
>
> Lucio Ricardo Montero Valenzuela
Thanks very much.
Lucio Montero.
--
From: "Justin A. Lemkul"
Sent: Wednesday, February 25, 2009 5:55 AM
To: "Discusson list for GROMACS users"
Subject: Re: [gmx-users] OPLS-AA topologies for ATP/ADP.
Lucio Ricard
Lucio Ricardo Montero Valenzuela wrote:
Does anybody have the topology files for ATP and/or ADP for the OPLS-AA
forcefield?. If not, how can I parameterize this molecules?.
Methods for parameterization can be found in the primary literature for the
force field. A few notes on this advanced
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