If using an amber forcefield and GTP/GDP you can use the parameters on
the following website. I have used the ATP/ADP ones and have had no
problems with many different systems and ATP/ADP conformations with
which I used to test these parameters.
http://www.pharmacy.manchester.ac.uk/bryce/amber#cof
Tom
Justin A. Lemkul wrote:
Carla Jamous wrote:
Thank you Justin,
but I ran a simulation before this one with GTP & it worked fine. GDP
& GTP parameters are identical except for GDP having less atoms.
This is why I can't understand why I don't get an integer charge while
I did in my previous simulation.
OK, but this still doesn't help anyone give you any advice. Please
refer to my previous post - which case applies to you: almost integer,
or way off?
It is also potentially faulty logic to suggest that GDP parameters can
be generated from GTP parameters by simply chopping off a phosphate.
Under most force field parameter sets, the charges on the beta-phosphate
will have to change since the electronic properties of the molecule are
now different.
-Justin
Carla
On Thu, Jan 21, 2010 at 2:15 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
Carla Jamous wrote:
Hi,
In order to run my simulation, I had to insert GDP parameters in
ffamber94 (the force field I'm using).
However, I'm having a problem with GDP charge.
the charge of every charge group in top file should be an
integer. But I'm getting a decimal charge which gives me
naturally a decimal total charge of my molecule.
I checked number of atoms, it's correct, their charge also.
But it seems it's having trouble adding charges & giving an
integer charge.
Does anyone have an idea where is the source of the problem?
What is the charge? If it is a small difference between an integer
and your charge (i.e., the difference between +1.9999 and +2) then
there is no problem. The issue there is the inherent limitation of
doing a lot of floating-point operations to sum the total charge.
If, however, you have a charge of +1.9256 when you wanted +2, then
your parameters are simply wrong.
-Justin
Thanks
Carla
-- ========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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