[gmx-users] Re: charges

Marc Baaden baaden at smplinux.de
Tue Oct 22 11:59:40 CEST 2002

>>> Erik Lindahl said:
 >> CHELPG is stable and good to very good even for large molecules. 

On a more general note, I would not really agree with this depending
on what you call a large molecule. We used to separate our molecules
in smaller fragments for charge derivation, as the electrostatic
potential might be biased towards a particular conformation and give
more weight to residues on the surface of the molecule if you choose
too large a fragment. This is of course only relevant if your molecule
has freely rotatable groups, not if it is very rigid.

You can also do several conformations of a fragment (eg cis, trans, gauche)
and check what the effect on the charges is, to see whether you can/
should average or have to make an informed choice based on the property
you want to look at.

Marc Baaden

 Dr. Marc Baaden - Laboratory of Molecular Biophysics, Oxford University
 mailto:baaden at smplinux.de  - ICQ# 11466242 -  http://www.marc-baaden.de
 FAX/Voice +49 697912 39550  -  Tel: +44 1865 275380  or  +33 609 843217

More information about the gromacs.org_gmx-users mailing list