[gmx-users] topology file format

[C. Klein]

Hello, 

Gromacs topology files include an [atomtypes] and an [atoms] section.
Both are mandatory. I suppose that every type of atom in the [atoms]
section should also be present in the [atomtypes] section? 

Now, there are charge definitions in both [atomtypes] and [atoms]
section. Can the charges be different? I frequently use my own charges
for certain atoms or residues, and thus this problem is very important
for me. If the charges can differ, then what are the "priority rules",
in other words, does the entry in the [atoms] section override the one
in the [atomtypes] section?

Thanks a lot, 

Chris Klein




-- 
Dr. C. Klein; cklein(at)pharma.anbi.ethz.ch
Dept. of Applied Biosciences, Pharmaceutical Chemistry
Swiss Federal Institute of Technology / ETH Zuerich
Winterthurerstr. 190
CH-8057 Zuerich
Phone: +41 1 6356062
FAX  : +41 1 6356884