[gmx-users] residual negative charge?

Ran Friedman r.friedman at bioc.uzh.ch
Fri Apr 18 19:30:56 CEST 2008

Hi Victor,

Assigning the right parameters for a molecule is a difficult task, and a
single run of PRODRG is usually just the beginning. Search the archives
and maybe also the wiki for more information, and read a few papers
where simulations of proteins were done with hetero-molecule if you
haven't done so already.

It's not a good idea to have a residual charge. You can obviously scale
this, but I would start by verifying that the PRODRG charges make sense
in any case.


Victor Manuel Rosas-Garcia wrote:
> Hello everybody,
> I'm trying to use gromacs to model an aza-type macrocycle (17 atoms around the ring).  The structure does not include any aminoacids or sugars so, I'm building the itp file by hand.  I started with a base topology from the PRODRG server and then added all the missing hydrogens (I want to use OPLS/AA). The problem is that, after assigning all the atom types as best as I could, I end up with a residual charge = -0.034.  The macrocycle itself should be neutral.  Does this mean I need to develop new parameters? Is there any way to fix this without reparametrizing?
> Thanx
> Victor M. Rosas García
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Ran Friedman
Postdoctoral Fellow
Computational Structural Biology Group (A. Caflisch)
Department of Biochemistry
University of Zurich
Winterthurerstrasse 190
CH-8057 Zurich, Switzerland
Tel. +41-44-6355593
Email: r.friedman at bioc.unizh.ch
Skype: ran.friedman

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