[gmx-users] Re: charges

[Erik Lindahl]

Graham Smith wrote:

>Sometimes I have altered the charges by hand using, for example, the
>differences between compounds containing corresponding charged and
>neutral groups in the force-field files. 
>
>I suppose the best thing would be to do a QM calculation, I think
>there are quite a few packages available.  
>
>I don't know very much about using any of them myself, but they
>probably have their own user groups: 
>
>Widely used, but expensive: 
>Gaussian: www.gaussian.com
>Jaguar: www.schrodinger.com
>

Personally, I prefer gaussian since we have it available on one of the 
supercomputing centers where I have an account. This way I don't have to 
worry about licensing or installing updated versions. But of course it 
would be nice if somebody has experience of a good free package!

The nice thing with gaussian is that newer versions allow you to just 
enter a set cartesian coordinates and the number of electrons for each 
atom, and then it can either optimize the structure or just derive 
partial charges (e.g. with CHELPG).

You can of course optimize things by using symmetries, etc, but this way 
I could calculate partial charges for the entire headgroup of 64 
different DPPC lipid conformations (about 35-40 atoms) in a couple of days.

Cheers,

Erik