[gmx-users] decimal charge instead of integer
carlajamous at gmail.com
Thu Jan 21 14:48:24 CET 2010
you were right, it doesn't work if I only take off one phosphate from GTP. I
was using the wrong parameters, now I have an integer total charge.
On Thu, Jan 21, 2010 at 2:36 PM, Thomas Piggot <t.piggot at bristol.ac.uk>wrote:
> 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.
> 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.
>>> On Thu, Jan 21, 2010 at 2:15 PM, Justin A. Lemkul <jalemkul at vt.edu<mailto:
>>> jalemkul at vt.edu>> wrote:
>>> Carla Jamous wrote:
>>> 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 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
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> Thomas Piggot
> University of Bristol, UK.
> gmx-users mailing list gmx-users at gromacs.org
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