[gmx-users] Ligand Parameters

[FyD]

Quoting Justin Lemkul <jalemkul at vt.edu>:

> I am interested in simulating some small molecules that involve oxygen in
> aromatic rings (which thus bears a +1 charge).  I tried to submit   
> one of these
> molecules to PRODRG, but got an error indicating that there were too  
>  many bonds
> to O.  I thought this issue might arise, due to the unusual condition of the
> oxygen (+1 charge, hybridization, etc.)  I have looked into the list  
>  to see if
> anyone had come across a similar problem, but I can't find an   
> explicit example.
>  I realize this odd case is probably limited by the developed force field
> parameters, which don't appear to include O+.  I have checked the   
> *.atp entries
> to confirm this.  I read on the archive that it might be possible to develop
> parameters using the ffamber ports (which I have) and using   
> ANTECHAMBER (which
> I have used) to get partial charges.  I would then have to create   
> some entries
> in the applicable .rtp file, etc, and otherwise do a lot of reading   
> in Chapter
> 5 of the manual :-)
>
> I realize this problem is not trivial, and I don't expect an easy   
> solution, but
> I was wondering if anyone out there had worked with O+ in their   
> molecules, and
> if they had any advice or topology building blocks that I might use as a
> template, seeing as none have been contributed online.
>
> I have also considered submitting an analog of my compound to PRODRG (normal
> aromatic ring instead of one containing O+) to get the dihedrals,   
> etc. and then
> re-calculating charges under ANTECHAMBER.  Any thoughts on that approach?

You might want to try to use the RESP ESP charge Derive (R.E.D.)  
version III - http://q4md-forcefieldtools.org/RED/.
You can generate RESP or ESP charge values for molecules and molecule  
fragments.
Eight charge models are now available...

regards, Francois