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 | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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