[gmx-users] decimal charge instead of integer

Thomas Piggot t.piggot at bristol.ac.uk
Thu Jan 21 14:36:45 CET 2010

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.
> -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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