dmobley at gmail.com
Thu Jul 26 18:19:56 CEST 2007
I can't help with most of your e-mail, but I can comment on part of it.
> After calculation of charges i am getting a small residual
> charge of 3e-06 for my ligand. My ligand should be neutral.
> Is this small residual going to impact my simulations?
You usually want to just round stuff so the sum is zero. i.e. adjust
the largest charge down by 3e-06 or something.
Of course, whether chelpg charges will be good for whatever you are
trying to do is another question entirely. The standard
parameterization cautions apply:
http://wiki.gromacs.org/index.php/Parameterization: You should not mix
and match force fields, and you should derive new parameters in a way
consistent with how the force field was parameterized.
> Is there any other changes that i need to make while using
> these new charges?
> Thanks in advance..Prasenjit
> Prasenjit Kumar Mukherjee
> Graduate Student
> Department of Medicinal Chemistry
> School of Pharmacy
> University of Mississippi
> Cell - 662 380 0146
> Office - 662 915 1286
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