[gmx-users] Iodine in ligand

[berka at natur.cuni.cz]

Hello GMXers,

I used PRODRG server for transforming pdb structure of 2-iodomelatonin 
into .itp ang .gro, but I found that Iodine in molecule has no charge. 
Which was strange.

I wodnered, what happened, so I changed my input and I put 
2-chloromelatonin into the same procedure and I got partial charges on 
chlorine.

Now I am about to use QM package for charge distribution, but I need to 
know which method and bases I should use.

Ive heard, that Amber is built over MP2/6-31G** base, but how si it in 
Gromos force field?

Nice day

Karel Berka