[gmx-users] decimal charge instead of integer

[Carla Jamous]

Thanks everyone,
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.

Carla

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.
>
> 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 <jalemkul at vt.edu<mailto:
>>> jalemkul at 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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>>>
>>
> --
> Thomas Piggot
> University of Bristol, UK.
>
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