[gmx-users] decimal charge instead of integer
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.
>> 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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