[gmx-users] Fwd: sds topology // prodrg vs. am1-bcc // charges

Louic Vermeer louic at louic.nl
Fri Aug 3 14:39:43 CEST 2007

Hi gromacs users,

I want to use a topology file for SDS and obviously I am not the first person 
doing simulations in SDS. Previous comments on this list suggested using the 
prodrg server, but I also read that the partial charges calculated by prodrg 
are not always reliable.

What would be the most intelligent thing to do?
1. use the prodrg topology file
2. use the prodrg file, but change the partial charges, using for example the 
am1-bcc method. This gives charge-groups that do not sum to a charge of zero 
(one group has +0.2 and another one -0.2, which seems quite a lot to me). On 
the other hand, the charges in the conjugated SO4 system are more distributed 
according to bcc, which seems better to me than the original prodrg topology.
3. hope for someone using this list to send me a "correct" topology file for 

I would also like to know whether charge-groups are used at all when using 
PME. Are they only for cut-off? I did not get that from the manual.

Thanks beforehand,
kind regards!

Louic Vermeer
PhD student
IPBS/CNRS Toulouse &
Biophysics group, Wageningen University


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